There is another reason FOR killing him that stands if you are more savvy to the nature of TES.
"Mantling", the best summary I'd seem goes something along the lines of "To walk like them until you become them". it seems odd to us, but in the TES universe when it comes to spirits, if something looks like a duck, walks like a duck and quacks like a duck, it becomes a duck. You've already seen it happen once - the Champion of Cyrodiil walked the path of Sheogorath until they
were Sheogorath.
Now, let's look at paarthunax...
- He's a dragon, like Alduin - Check
- He wants to lead the other dragons like Alduin - Check
- He has a human cult who will obey his command (Greybeards), like Alduin did (The dragon priests) - Check
- He has an intrest in humans and dragons working together (like Alduin once ENFORCED) - Check
And there may be other details I've overlooked, but the key thing is Paarthunax has already begun to walk a path that is superficially close to that of Alduin. The Champion of Cyrodiil's path may have differed greatly from that of Sheogorath in the early days of his career (During Oblivion), but 200 years down the line, the CoC and Sheogorath are indstuinguishable, he has been mantled. In 200 years time might Paarthunax not have simply replaced Alduin? - The world is
meant to be eaten, it
needs it's Alduin, and there is an Alduin shaped hole waitting to be filled...
Either way i havn't killed Paarthunax personally, but from a lore perspective there is a very real danger posed by his existance if you are savvy with the physics of the setting