I finished the companions questline but when i try to ask Aela for more work she keeps giving me those animal extermination quests. I think this is because i married her, although i am not sure. I also have all the remaining witch heads in my inventory (i heard it was a solution to fix this) but it does not help.
Is there any other ways to fix this?

Keep trying. I marred Aela and did not have that problem. Hircine will initiate eventually I should think. It may be related to your level. There was a glitch in the quest that has been patched already and the patch worked. It invovolved a fatal error retrieving a totem from Haemars Shame. Really lame since totems don't always spawn in Haemars shame at all. But if one did and you already did Daedras best friend..... Crash This is fixed, even repaired if you had this error already.

The problem with marrying Aela I have is

• She stops cooking for you and does not function at all in Jorvaskr. The cooking dialogue has not appearred since the 5th meal she prepared.
  
• If you sell her items, her inventory gets so heavy she cannot carry items for you on quests any longer......really lame

About the witch heads. Strange but I had no problem storing them after completing that quest line. In the final chamber however after destroying the werewolf spirit, I activated the pedestal again and it asks if you no longer wish to be a werewolf. I chose to remain werewolf. This may be crucial to deactivating the heads as quest items as they can be used to cure you of werewolfism.