Not necessarily. If being a vampire would exclude me from Meridia's quest, it might open up further quest material from Molag Bal, who is the creator of vampires.
It could be true also that Meridia didn't know my true nature, however unlikely that seems.
The vampire who hunts vampires isn't an unknown character: Blade from the Marvel comics, Jander Sunstar from the D&D novels, Constantine from Robin McKinely's
Sunshine, (Vampire Hunter) D from the manga series and anime movies, et cetera.
It goes against TES openness to put in lots of restrictions. Players are welcome to restrict themselves, but what works for one person might not work for another. I rarely join more than one guild with a character, but my wife joins everything.
But on the other hand, who says Daedric Princes can't be hypocrites?

Sheogorath.