I love these stories. I have a hundred of them. I had two trolls chase me into a swamp once and, as with the OP, they awoke an abomination. I think they'd have won but a bunch of draugr chimed in and the blueboys went down.

To the OP. As soon as you enter the crpyt, stay on the ledge and build a fire. If any mobs are lurking free, then they can't get to you there and you can safely mow them down with a bow. Use a 2 handed mace to kill 95% of mobs lurking behind the muddy piles before you even have to face them. You can usually destroy spawners as well with enough whacks (you'll here the explosion). Excavate carefully so you can see any remaining mobs but so that they can't jump out at you. Pew pew or whack whack with stagbreaker. Get an iron 2h mace asap, just for this purpose.

Once you get the knack, sunken crypts are soooo easy.