A few things.
It is customary for the refund to be issued after the animal has been received by the seller in the event of a return. Whether the buyer is trusting enough to do that depends on various things, but that is the norm. If not willing to return the animal prior to the refund, the process usually reaches its end. While some sellers will occasionally extend an uncommon courtesy of refunding ahead of a return, it is a departure from what is typical because it opens the seller up to a scam. While that should not apply to you as you know yourself, there are indeed quite a few buyers who do set out ahead of time to run scams like that against sellers. I would not blame you either way, but I would probably return the animal for a full refund if I were in your shoes, as I do not set out to buy undeclared issues. I will buy (or sell...or gift/donate, depending) compromised animals from time to time with any issues fully explained and shared, but nothing was declared here. I may have overlooked it and I apologize in advance if I did, but you paid $100 + $450 + fees (I am not sure why you are being charged additional fees, but okay). Supposing that equals the $565 shown as the stated refund amount, how would the return shipping be handled? Are they providing a label for the shipment? I ask because you should not be paying for return shipping of an animal that came in not as described relative to its condition as known at the time of purchase. If the return and refund option would be chosen by you at this point, it should be 1) they provide you with a label, 2) you ship the animal back, and 3) they immediately refund the $565. That or you keep the snake and do whatever you have to do in terms of care. Again, I would not fault you either way on that, but I would personally choose the return and refund. If you do choose the return option, make sure that it is crystal clear that you will not be footing the bill for return shipping.
I am not sure whether they noticed or not. It is pretty hard to miss when handling such an animal. I have seen things get hidden in folds of skin or in leg pockets for various reptiles before, but an "unhappy" vent area is usually glaring to me. That said, if the person/people were in a rush and did zero physical inspection or the animal turned "just so" while being glanced at, maybe (maybe) it could have gone unnoticed. However, regardless of that, it was present before/upon receipt by you and that makes it the seller's responsibility. I think both of the options for resolution you offered were reasonable with the return-for-full-refund option being standard and obvious for the hobby.
Removal of complaints is a different matter. They would not be removed here and removing them from various FB review groups is often grounds for being blocked from said groups (whether stated or not in their rules; every place is a little different, but that is common practice).
since they had your $500.00 already ? 
" ... it wasn't like that when we packed it ... " 
