It is just sad that your town has gotten to the point that you cant keep pets in your own home without your local government getting involved. As said previously, notify them of your husband's harassment of you through their officials.
Sadly, if you have to apply for a permit for anything you are asking permission from government (which implies that it could be denied). It seems that your local government doesnt see the need for any substantive reason to deny permits (and might not legally need any).
It sounds like you must have a very understanding landlord, youre lucky. You should be sure to remember to thank him, he might be having a difficult week as well.
Best of luck with your appeal. I would suggest that you never let them into your home again without the proper legal paperwork in hand - that includes when he comes to see if the bunny is gone (be sure that it is anyway).