In my own experience, a noisy thrust bearing has never been more of a problem than the irritating noise it makes. I've only ever replaced one flywheel and it was a G60 one to replace my standard 1.9tdi wheel. Not that i'm questioning anyone else's experience with them of course!
Replacing the thrust bearing is a pretty easy job to do yourself if it's bothering you that much. I'd just wait till your clutch gives up though
- seeing as you seem to have done it quite recently, that could be a while :p