As I've noted in the past, a lot of modern-day Reformed people do not agree with the observation that denominations divided from each other in the context of a presbyterian system of church government are refusing to recognize each others' de jure legitimacy and authority, even though this observation seems to follow pretty straightforwardly from the basics of a presbyterian view of the visible church.
I have argued that one of the reasons for this is that many modern Reformed people are not purely presbyterian. They have diluted their presbyterianism with a dose of congregationalism, resulting in what is really a semi-congregationalist view of the nature of the church. In a presbyterian view of the church, all true churches have a moral obligation to be in formal communion with each other under binding councils, but this idea has been somewhat (though not entirely) lost sight of in much of the modern Reformed world.
One argument (among others I've previously noted) used by Reformed people to avoid affirming that denominations reject each others' de jure legitimacy and authority while still claiming to be presbyterian goes like this: "Look, we in the PCA (for example) do indeed recognize the de jure legitimacy and authority of the OPC, the RCUS, the RPCNA, etc. We are not congregationalists. Congregationalists hold that churches need not be joined in formal unity under binding councils. But we, being presbyterian, do hold that one, formal, worldwide church unified under binding councils is the ideal of what the church should be like. However, the world is in a fallen, sinful, imperfect condition. Ideals cannot always be met. The church has an obligation to pursue not only the unity of the church, but her purity as well. Therefore, while we do indeed grant de jure legitimacy to other denominations, we cannot at this time be fully united with them because of differences in doctrine and practice, etc. But we are still presbyterian, because we believe that is the ideal we should be striving towards."
Does this response preserve the presbyterian status of those who make this argument? Does it justify presbyterians in making the claim to recognize de jure legitimacy in other denominations while refraining from formal union with them?
While the argument is quite correct in noting that the purity as well as the unity of the church is to be sought, and that a concern for that purity does indeed make it wrong for more pure denominations to join with less pure ones, yet the argument still evinces a semi-congregationalist rather than a purely presbyterian view of the nature of the church.
An analogy may help to bring this out. Imagine that a family has adopted a child. The paperwork has just been completed, all the documents have been signed, and it is now official: The child is fully, legally recognized as an adopted part of the family. The child is excited to be able to go home with his new family.
"I'm so excited to be going home with you today!" says the child.
"Wait a minute!" says his new father. "Sure, you've been adopted, and we fully recognize your adopted status; but that doesn't mean that right now you get to come home and begin being a full part of our family. We need to give this much more time--perhaps a few years at least--to make sure you are compatible with our family before we bring you home. Don't be naive. Ideally, families ought to bring their adopted children home with them. But this is not an ideal world. It is a world full of imperfections. Adoption doesn't mean you get to be fully treated as our child right away. It simply means that we need to strive with good effort, and yet cautiously, towards hopefully, someday, realizing the full ideal of incorporating you into our family. In the meantime, perhaps you can come and visit for an evening once a month or so, while still living in the orphanage."
What is the child going to think of this way of looking at things? At the very least, he is probably going to say to the father, "I don't think you really understand what 'adoption' means. You can't grant the status of 'adopted' while refusing to grant with it all the rights and responsibilities it entails."
And that is what I would say to those who make the argument I articulated above. "You simply do not understand what 'de jure legitimacy' means in a presbyterian system." To fully recognize the de jure legitimacy of a denomination is to grant that all of its church courts and officers, right now, have legal authority to function as such. They have a right to be treated as fully legitimate officers and church courts. Since, in a presbyterian system, all church officers and courts have a right and a responsibility to be in formal communion with each other under binding councils (officers functioning together in united sessions, sessions united in common presbyteries, united in common national councils, united in a common general or ecumenical council), to grant de jure legitimacy to a denomination is to say, "This denomination has, right now, a right to be in full, formal communion with us and to be invited to join with us under binding councils." To say that one recognizes the de jure legitimacy and authority of a denomination, while at the same time refusing right now to grant them the full rights that essentially accompany that status, is either to be intentionally unjust or to manifest a lack of understanding of the presbyterian nature of the visible church.
Granting de jure legitimacy, just like granting the status of "adopted," does not signify an intention of working towards some kind of full relationship sometime, hopefully, in the future. It signifies a present granting of a status that inherently implies certain rights and responsibilities in the present. It is inherently the right of a de jure church court and its de jure officers to be given full authority as such in the de jure, binding councils and courts of the church; and it is inherently the responsibility of de jure courts and officers to join in formal union with the rest of the de jure church in order to exercise their authority in conjunction with the whole church. Therefore, to refuse to grant these rights and responsibilities to professing de jure courts and officers is really to deny their de jure legitimacy--in a biblical, presbyterian system. In congregationalism, however, there is no necessity for de jure courts and officers to be in communion with each other beyond the congregational level.
Therefore, the users of the argument under discussion are not purely congregationalist, nor are they purely presbyterian. They are somewhere in between, which is why I call their view "semi-congregationalism." (I could also call their view semi-presbyterianism, of course, but I choose to emphasize their departure from pure presbyterianism since they claim to be presbyterian and have presbyterian historical roots.)
It is quite right to say that there appear to be many de facto manifestations of the Body of Christ in many different denominations. And it is correct to say that this gives us all a moral obligation to work towards the unity of all Christians in the world so far as we are capable of doing so without neglecting other duties. However, the fact is that the present reality of denominational division means that all of our different presbyterian denominations are out of full communion with each other and do not recognize each others' de jure legitimacy and authority. This is the only presbyterian way to look at the situation. Perhaps understanding the full weight of what denominational division implies can help motivate us all more to do what we can to remedy this sad situation.
UPDATE 5/16/13: See here for a dialogue that further illustrates the above reasoning.