Well Harkon was more of a 'demented, crazed, power hungry, obsessed with the sun that is so unhealthy that he should be in an asylum' kind of deal, but yea. What would happen though if you could join harkan? Serana would probably be demolished, along with what's-her-face-who-likes-to-lock-up-daughter-for-fun who happens to also be very paranoid.
But that is interesting... what could have happened... What would happen to the sun? It is a fact that when you blot out the sun it only lasts a day but still.. What would happen if you sided with Harkon, vampires being immune to the sun (sorry if I didn't read the basic plan of action on Harkon's terms) would be kinda... Chaotic. But I like chaos... I think it's fun... Hearing people scream. >_> I'm a demented person... Yes.
But if you were evil.. Wouldn't you want to dispose of Harkon yourself, and plan a new order of vampires, ones who make mortals as their pets or something? Hm... I'm gonna chew on some pretzels on this... This is an interesting 'what-if'.