A.2.2 I changed several thousand files at once and now Magit is unusable

Magit is currently not expected to work under such conditions. It sure would be nice if it did, and v2.5 will hopefully be a big step into that direction. But it might take until v3.1 to accomplish fully satisfactory performance, because that requires some heavy refactoring.

But for now we recommend you use the command line to complete this one commit. Also see Performance.