...100% CPU while performing an fsck...

Yeah, I noticed that myself today. I'll take a quick look. Medium term, I plan on getting the source profiler to work, which should give me some hotspots to look at.

any chance of emptool ever getting the code that fixes corrupt database issues?

I don't know. If you have specific things that can cause it to crash, report them in the Bug Reports forum. They'll get looked at.