Yup. Some dealers will balance and most aftermarket rotor companies do (for a price I am sure). However, if it was good before and now is bad, there might be dirt behind the rub bars that have thrown it out.
I have to Balance the rotors on our CR960 this year because The devider between the rotors came loose and went into one of them. The cost to do both of them is $800 at Atom Jet in Brandon, and Precision Farm Parts will do them for $600. I have heard Mazer in Brandon will not sell even a new CR without taking the rotors to Atom Jet to balance first.
I second the belt idea. If you have ever plugged the rotor you may have a bad spot on the belt. This will not be real eveident at low rotor rpm but when you get into the 1100 plus you really feel it. I was worried as well but it ended up being a belt.
My money is on the belt too, run it up so its vibrating and jump out and see if the belt is whipping, there could be a bit of rust on the shieves which wont be helping, also check the belt for wear, if it is worn on the edges too much the shieves cant keep it tight, i would be checking the simple stuff before pulling the rotors out