It is quite possible that Mako is indeed a clone. Remember, she's in a universe with a planet that can create tens of thousands of clones, and seeing how Kamino wasn't removed from the galactic republic's databanks until just prior to the prequel trilogy, it's just as plausible for the republic to be conducting experiments on said planet.
With that in mind, is it bad if she was a clone? My answer: HELL NO! It wouldn't make her any less of a person. After all, as we all know, there was a man who was born a clone who grew up to become one of the most recognized and most powerful bounty hunters to grace the galaxy.