[Travis Covington]

Any quality component or assembly, when disassembled and reassembled by a competent person, should function nearly the same as new. Any performance differences would be negligible, and would be apparent across all of the unmodified parts or assemblies of its kind. I don't see how taking something apart is "modifying" it in any sense of the word.

Edit: In all honesty though, I think removing the shaft is overkill. A dremel cutoff wheel works just fine and does no damage to the motor or the remaining shaft if you are cautious to avoid excessive temperatures when cutting.