Hmm... I've dove with Amigos, I can't say anything about their equipment as I've used my own but their tanks were FINE. The divemasters were FINE too. The corals and fishes were a plenty.. I've eaten their food as well, YUMMY! Although I didn't eat much of their chicken as I'm a vegetarian, but they had other options, potato salad, rice, etc. The coconut pie was SO GOOD that I wanted another piece. They had plenty of beverage to go around as well. They're very environmentally conscious as well, their boat stopped to pick up a big piece of garbage floating in the middle of the ocean.
I've also dove with other operations in San Pedro, they were FINE too. Just because Amigos has the best reputation does not mean other dive ops suck.
What I would've done if I were you- get a list of exactly how much everything costs, ask a lot of questions, etc before you even make reservations! Not that I'm saying it was your fault but... You need to be well informed before you make any decisions. Research online and get opinions from other people.
Honestly.... Hotels aren't responsible for warning you about botflies, mosquitoes, etc just like in the US.. It's all common sense. I'm sorry you failed to realize that there are actually bugs in Belize. I found out about no-see-ums for the first time when I went to Belize last year, oh man! I looked like I had measles but I learned my lesson and brought mineral oil with me the next time around.
You should contact your credit card company, they'll remove these charges if you didn't approve of them.