Yes, which to me was stupid. Shouldnt that be part of the main quest?
In a way, yes. but think of it this way.
The Dawnguard was never a concern to the vampires in the past few centuries. this new group of ragtag hunters certainly wouldn't pose a serious enough threat to the most powerful family of vampires in skyrim (maybe even all of tamriel) for them to put their destruction before fulfilling a millennia old prophecy. In fact, Harkon's obsession with this prophecy, along with his goal being finally in reach, probably made him not even notice the Dawnguard reforming. this is why his less busy underlings were charged with stopping those who opposed them. Being as arrogant as most of them are helps to support this theory