Why would Martin kill someone who helped him?

Because if had a rule against killing those who helped him then he would have to let Alduin live too.

Still, Paarthunax has changed

Doesn't change what he did.

I never killed him and never will.
He was allied with Alduin, but he redeemed himself when he helped those humans.
I will shout both Delphine and Esbern from Sky Haven and let my followers live in the place.

Does it changed what the Doctor would have done? He redeemed himself by not burning Gallifrey

Alduin helped him as well, why did we kill him again?

Paarthurnax was instrumental in the killing of hundreds if not thousands of people, just because he's been chillin up on that mountain for awhile doesn't mean he won't do it again. It is in the nature of all dragons to rule over 'lesser' creatures. I figured the time of the dragons in Tamriel was over, and killing just one more dragon is a small price to pay to ensure that they were never a threat again.

The guy won't need to, he's already doing it. By teaching his fellow Dovah the Way of the. Voice, he's suppressing their inner nature and living up to his name.

In all honesty, I fail to see any non-roleplay advantage to be had from killing Paarthurnax. It's not like you're missing out on anything other than dragon hunts, which you can do anyways.

There's actually no non-roleplay advantage to letting him live either, the quest is really kind of pointless in my opinion...