Never let continuity override telling a good story. Going off-book is as much a part of D&D than anything else, and considering how many house rules were part of BG 1 and 2, I'm willing to give this a chance.
I could argue going off too much ruins a story because it breaks immersion. Vampires have a distinct power level and changing it because “story” is lazy writing.
I'm gonna say it: If someone came to me as a DM with Astarion as a PC, I'd say yeah. It's a pretty good character concept, and I've played with way weirder, and saying "sure yeah you can be a vampire pretty much in name if it helps with this cool subplot I'm down for that" seems like the more reasonable thing than saying "NO vampires HAVE TO BE challenge rating 5 and THEY CAN'T DO ANYTHING BUT EAT BABIES", wouldn't you think?