Ok, I wouldn't know too much about this.
But, for what it's worth, I do know that John Petrucci likes to work out a lot, and it doesn't seem to have done him any harm.
I'd guess you just have to use common sense and don't start lifting weights that have crappy and rough bars to grip them with, and just generally taking care of what you're doing.
Also look out for things that would induce RSI or that will cause inflamation. After all, if you are consistently putting yourself out of guitar playing action for a while, your development would be slow and maybe even impeded.