I enabled AudioSnap for a 3 minutes long clip in a big project (25 audio tracks, 4.5 hours). Is there a decent way to undo this, other than going to older project version and avoiding AudioSnap? Pressing Ctrl-Z does not do the thing. Problem is that project size jumped from 2 MB to 97.5 MB and now saving takes 10-15 seconds and I have Auto-Save enabled with aggressive settings.

97.5 Mb is not big at all. You may be mistaken Megabite for Gigibite. Audio snap will increase your project size. 

The longer save time is because audio snap is enabled and it probably need to save each transient or something like that.

To get rid  of this, other than deleting the audio snap, you just need to render everything that audio snap is enabled on. Then delete the audio snap.

CJ

I render or bounce the track after AudioSnap has done its stuff.  That frees things up.
Right click on the track and hit B on your keyboard.