if you look at the exhaust side there is usually part of the shaft machined off to balance them out. i would think it would have to be balanced as an assembly. sure the new wheel may be balanced but the whole assembly together probably won't be. when something is spinning over 100,000RPMs its not ounces, its grams off can wreak havvoc... just my $.02
While what you are describing may be the ideal method, there are many, MANY turbos that have been pieced together in people's garages that have worked without balancing the assembly.
HX35s are a dime a dozen, I wouldn't waste my time or money on one so I'd just replace the wheel and see how well it works. If it fails, get another one.