Yes, landlord can charge for companion animal deposit. Remember, just because it's a great companion, doesn't mean it's not going to shed, go to the bathroom if not taken out, etc. Being a recent dog lover myself (see my picture-that's actually my puppy and my hand - he's very friendly and that picture is very funny if you know my puppy) it may seem unfair, but it's still allowed.
Under these facts I don't see retaliatory behavior.
The above is general information since I haven't seen rental contracts, nor do I know all the facts so don't take it as specific advice.
Good luck on your situation.
A landlord has to accomodate your companiion animal but is alao allowed to get a deposit for damage to the premises, and there doesn't seem to be anything retaliatory about them asking you for a deposit. If the landlord asks you to move in month 7, or takes other action against you or your pet and you think it's because of the pet, then you may have something to complaint about, but right now, it seems like the landlord just wants to protect the property from pet-caused damages.
Disclaimer: Please note that this answer does not constitute legal advice, and should not be relied on, since each state has different laws, each situation is fact specific, and it is impossible to evaluate a legal problem without a comprehensive consultation and review of all the facts and documents at issue. This answer does not create an attorney-client relationship.