Apparently MJPolyTools causes some strange properties in the hypergraph that are a pain to clean up. Is there a better edge splitting plugin that can split only selected edges? (I use the split ring tool built in, but it only splits whole rings).

Once you have entered the split edge ring tool hold down Ctrl+Shift+RMB and a menu will appear, turn off auto complete and the tool lets you select edges instead of doing the whole ring. Press y to except your split, further information can be found in the Maya7 help file on split edge ring, there are some neat splits you can do depending on your selection.

is it bad enough that deleting the history and optimizing scene file doesn't clean things up? how about exporting/reimporting an .obj of your model periodically?

i'm guessing you have an earlier version of maya than 7. koshigaya, open maya toolbox, and bonus game have the tools you're looking for.