I honestly can't see how jQuery dictate how you architect your code. jQuery is a DOM manipulating library and AJAX library. It is not a framework. It doesn't force you to organize your code in any particular way. You know that jQuery is not forcing you to not write everything in a single main function, right?
So I fail to see how using $('#...").foo() in your large project is going to be harder to maintain than rolling your own DOM manipulating library.
If all I'm doing is domConstruct.put() instead of $().append() then of course you're right. Dojo in addition to browser normalization and other good things that jQuery does, suggests a structure that works pretty well. jQuery to my knowledge does not.
So I fail to see how using $('#...").foo() in your large project is going to be harder to maintain than rolling your own DOM manipulating library.