You are not alone! I've seen this come up many, many times. I have found that it's easier to get guests to accept a refund, than an additional fee, so my "workaround" is to set my cleaning fee as a pet fee and then note that if a guest is not bringing a pet I can either do a special offer or change reservation with a refund.
This is may hurt my bookings if people don't read the description and think my cleaning fee is too high, but I'd rather have that money in the bank than have to keep asking the guest for more. And even my pet cleaning fee isn't outrageous, but I'm happy to attract dog owners as there aren't many properties here that do in my price range.
Why they can't just add a pet fee like an extra guest fee I don't understand! It can't be that hard!