I don't know why the rep wouldn't be working. What browsers are y'all using?
The thing about rep vs. thanks is that rep is a built in vBulletin feature, and thanks isn't. I think there's a vbul hack that will allow you to give thanks, but remember, the more hacks/plugins/etc on the site, the more slowly it loads for everyone.
Personally -- I'm not speaking as a mod, here -- I don't see a problem with having the ability to leave negative feedback. I've never actually done it though.
But it seems like the membership here is by and large mature enough to handle it.