While in the Underforge, I knocked out Aela to take her blood and she was permanently put into werewolf form. Is there is way I can transform her back?
Go into Console.
CLICK DIRECTLY ON AELA. You should get a number string 0001a696 or 0001a697 coming up.
Type in (including the space): setrace nordrace
Worked for me in the Underforge, giving me back my Expert Archer trainer.
If you're on the PC, console commands may fix the problem for you: Open the console, click on Aela, enter the command "disable" (she'll promptly vanish), then immediately run the command "enable".
This process worked for me when Lydia got "stuck" in a two-handed combat stance without her weapon, and was completely unable to do anything at all except follow me and get in my way. I've never had your particular problem, but "resetting" followers like this seems to work in a wide range of cases. (Plus, as a bonus, your follower will "level up" as if you had just met her!)