I'd totally put $1000 wheels on a $1000 bike if I thought the wheels were worth that. I find it unlikely that I'll pay more than $300 for wheels anytime soon, though.
You can transfer them to a new bike later, and that bike won't come with $1000 wheels either. Also, if it's already a decent quality aluminum frame, the difference between that frame and another is pretty incremental. And, for me at least, component selection is something that seems to get more and more specific to me the more I ride. Unless I'm getting a bike in a different genre from the ones I already own, I don't see myself buying complete bikes in the future.
If the Fisher has a nice frame, I don't see any problem with replacing things piecemeal, with nice stuff, over a long period of time. If you're upgrading to upgrade, though, rather than replacing worn or broken components as they fail, maybe save the money and wait until you have enough to get a really nice complete bike - it'll probably be cheaper.
What wheels are on that bike, anyway? Bontrager makes everything from pretty cheap to pretty fancy.