He's been resting on a remote mountain-top, in completely seclusion, teaching a group of old mean how *not* to use their powers for the past several thousand years. Furthermore, after the main quest, he's going to be one of the last two Dragons. Destroying him is like destroying a priceless work of art, or history. So much knowledge, lost, simple because people fear something me *might* do, even though he's given every indication that he has no desire, or intention for conquest or domination. On another note, he's only one Dragon. Old, yes, powerful, yes, but there's a limit to the amount of damage he can do before he's stopped.
What better way to control the dangerous Nords that have learned the Thu'um than teaching them a new philosophy to never use it in violence?
Granted, he does teach the player Dragonrend, but that could just be a manipulation. It's too early to say either way if Parthurnax is truly redeemed or not. I agree with you about killing him though, and when you go to Angvier after he summarizes the disgusting act you've done quite nicely.
Also, "he's going to be one of the last two Dragons." What indication is there of that?