I found one of their dive guides to be rather intrusive. Not all of them though. Most of them were fine.
Happened to me once. Following a dive on the Duane. There were maybe a dozen of us on the line at the safety stop. I had just completed a solo dive, there was a Rainbow Reef DM right below me. He caught a glimpse of my tank pressure (about 200 psi) and frantically tried to shove his octo in my mouth. I casually waved him off, pointing to my (full) back mounted pony bottle. He just didn't get it. On the boat I approached him and explained that if I have more than 200 psi at my safety stop I'm wasting perfectly good gas, as my pony is my reserve, he shrugged me off. As we approached the dock, one of their PR people did the whole speech about how they hoped everyone had a great dive and can they please support them with a positive review and if there were any problems please let him know. I told him about my experience, he was understanding and sympathetic and sort of nodded when I pointed out the DM in question as if he had issues with him before.
For whatever that's worth.
Every diver on the boat was broken down into groups of 5-6 and every group had a guide.
That's different than what you said- which was that
a guide is required. You could have easily stated, as I would have done that you prefer to dive alone (if certified and equipped), or with your buddy or whatever. You just went along with it. Not that there's anything wrong with that but you're spreading fake news.
It's no different then when you're diving alone on a boat and the crew tries to give you a whole lot of medical and legal liability and a good chance to mess up a perfectly good dive by saying "you're going to buddy with this random diver of unknown skills, experience and fitness, and if they mess up and there's an accident you can expect to be sued". "Um, no I'm not, my buddy is that bright yellow 19 cf cylinder strapped to my main tank". Unless she's a cute young hottie in which case I will say "Would you prefer to lead or follow".
We were very much wanting to dive the Duane and the Bibb but conditions didn’t allow for it.
We were told strong currents made those sites “un-dive-able” while we were there.
The Bibb is rarely dived because it's deep and it's sideways orientation makes for a "less than fun" dive, and because of the orientation there aren't many penetration opportunities. There's also not a lot of fish on it. The Duane is much better, upright, loaded with fish and coral growth which is interesting given how close the wrecks are to each other. I have trouble getting to the Duane as well, because it's in an area where there's a lot of current and most dive charters don't want to risk dropping a bunch of divers on it as they may get blown off it.
There used to be a charter in Tavernier called "Divercity" or something like that. A small mom-pop operation. They wouldn't scare off the Duane easily, in fact they'd drop divers at one end (usually the stern) and pick them up at the bow where the current would take them. That was a great dive.