It does kind of almost sort of in a way partially make sense if you suspend a resoectable amount of disbelief. Section 31 wanted his genius but not the associated baggage. Though why they didn't just compromise and use one of the 72 others is unclear.
… because the super-secret branch of Star Fleet was worried its project to subvert the legitimate government of the Federation, build an armada of hyper-advanced weaponry, and launch a preemptive invasion of conquest against neighboring powers might suffer from some bad press if they have on staff a secret agent who looks like a half-forgotten warlord who died centuries ago …
My sentiments exactly.