My gut feeling is that this violates the GPL, because the application "forms a single program" with the commercial plugin and thus the "combination of the GPL-covered plug-in with the non-free main program would violate the GPL".
It depends what you mean when you say this violates the GPL. Creating such a system does not violate the GPL -- you can freely use software licensed to you under the GPL to create proprietary software. That's one aspect of freedom. The licensing issue only arises when you then want to distribute the result.
But who violates it? Are users violating the GPL upon loading the GPL library along with the MIT plugin?
That is indeed the crux of the question. Again, however, it is not forming a work combining GPL and proprietary code that violates the GPL, so end users who only load both plugins into the program do not thereby violate the GPL.
Suppose different people develop each part---does the commercial plugin developer violate the GPL, even though they have no knowledge of the MIT plugin, perhaps because it was not developed yet? Does the MIT plugin developer violate the GPL, simply because a commercial plugin exists, despite that MIT is compatible with GPL?
IANAL, but I am fairly confident that one independent group's actions in developing a plugin for your software does not place any obligations on you or on other independent plugin developers, regardless of the license under which any of the independent groups distribute their software. There are still some ways you might run into trouble, however, such as
one or more of the plugin-developer groups are not really independent of you or of each other. If there is any kind of agency, sponsorship, or other special relationship there then at best the situation is shady.
your own group (re)distributes one or more of the plugins, whether together with or separately from the main package. That might be construed as distributing the combined work, which would be a GPL violation if the combination is not licensed in a GPL-compatible way.
your licensees need to obtain one or both plugins in order to use your software for its ordinary purposes. In that case it really is a combined work, and attempting to avoid licensing obligations via distribution tricks is at best unethical. On the other hand, this would also suggest that there is indeed some kind of special relationship between you and the other groups involved, as discussed earlier.
There are likely other potential pitfalls.