I have figured out, somewhat, ways to improve performance. It is still an order of magnitude slower than ArcObjects, which is going to be a problem for us and our clients (end-users of my add-in).
Since we have no need for any type of undo, I am forgoing the edit operation for the Row.Store() method.
Adding attribute indexes for the fields getting updated speeds up performance a lot. This, as far as I can tell, can be done only using geoprocessing and not via the SDK.
Row.Store() really speeds things up when I need to write to multiple fields - it takes roughly the same amount of time to write to one field as it does three.
Strangely, it is actually quicker to write to a shapefile (dbf table) than it is to a geodatabase (the tables are otherwise identical). Writing 96,000 records to a shapefile took 2:49, while the gdb took 3:34. ArcObjects could write to the same shapefile in about 10 seconds.
Any tips to make this faster (or, improvements in the SDK) would be greatly appreciated.