Villain? Kalpa's are not bad. Stopping them from ending is not good, it's just different. Parthalax explains this in Skyrim.
The other depiction of Mehrunes' origin paints him in an even more positive light, but what else would you expect from the writings of a Daedra-worshipper?
But really, the first Aldudagga fight is about the transgression of the Greedy Man, who is probably Shor in this context (he's trapped in and outside of Kalpas, and hides under a mountain that isn't there - sounds like both Snow-Throat and Red Mountain). The Leaper Demon just makes a bargain with him, and suffers for it. I'm still not sure what the mythic significance of all this "world getting bigger to stretch Alduin's stomach" is.