With Prism you have the option to use Unity and/or MEF as the IoC/DI framework....it's also quite extensible...so you can plugin different IoC containers if you wish.
Some of the problems with leaks can usually come down to not using WPF in a certain way e.g. need to use Weak delegates / Weak event patterns, etc.
You could roll your own plug-in framework using MEF, but you'll probably need to re-invent some of the things Prism already does for you e.g. an EventAggregator, etc.
You could pick an alternative framework, they all have their strengths and weaknesses.
There's another Microsoft technology that is geared to supporting plug-ins namely, System.AddIn/Managed Add-in Framework (MAF)....but you have to put in a bit more scaffolding.
Someone has come up with a framework that uses MEF here:
If you want to look at an Enterprise size project with their own very plugable/modular architecture then look at SharpDevelop for inspiration.
....and it's not beyond the bounds of possibility, if you really want, to combine the best bits from several frameworks.