Unfortunately.. I don't sync my facebook contacts onto my phone. I prefer to keep facebook completely separate. So I'm not sure how much help I can be on this one. (Drod might be able to assist you more)...
Seph, I haven't installed the Facebook for Android yet as I am afraid they will change every dang contact which I want to keep separate, also. Do you recall when you install Facebook, if the contacts will change like they do on HTC Sense? Thanks.
Hmm, so... there's the facebook that comes with the stock phone that's integrated with contacts... that I simply do not use. Then there's the market facebook app., which I DO have installed. Nothing shows up differently in my contacts due to that facebook application. What did HTC Sense change exactly? If it made changes to the contacts on the phone itself, I can say that the market facebook app seems to not affect us in that way!
OH, and suggest for testing yourself! Take a backup from within recovery (nandroid backup), and THEN install it, then test thoroughly. If it does something you're not happy with, just restore. Can't tell you how many times I've done this while testing...