Interesting first time post (and user name!), and I too would be interested in hearing what the company will do for you, but I might have waited just a bit to find out before sharing this limited information.
Even the best Live Aboard ships as well as Land Based Resorts do suffer occasional problems. When the problems are mechanical in nature, usually the best possible accommodations are offered to allow for available alternative diving, possibly chartering local dive boats to provide some relief. I assume that is what you were saying.
If one finds that unacceptable, a good course of action might have been to discuss your alternate ideas with the Captain. It would seem that the only difference in the cost of your chosen option would have been the transportation to and from your floating hotel. Not a big difference dollarwise, and I would have taken that up with them as well.
I had a similar experience in the Indian Ocean. As we arrived at the dock of the wooden dive boat vessel, they were ripping out the freshly charred galley after a fire had caused some damage. The local fire department, such as it was- two guys and a hand pump on wheels, were still there. There we were, 12 time zones away from home, very little English being spoken, and somehow we managed to get in 6 days of diving aboard local day boats. Not what we had hoped or paid for, but the owner of the boat hosted us every night for dinner and invited us back for another try. I got to like curry. Genuine concern coupled with that offer did bring us back (with no concerns) a second time. It's all good.
Still, a liveabaord dive vacation is what you went there for, and I am sure that they would have told you not to fly in if they had known this wasn't going to be resolved quickly. I think when any of us looks at a mechanical issue, we all assume that everything will go well and be resolved post haste. At least that's what we try for, and with my own Nekton experiences, that has been quite the case.
I have been aboard every liveaboard in the Caribbean that I am aware of (from magazines, the internet and trade shows), I have been diving from many of those, some no longer in service in the Caribbean, some long lost to the deep. Not every liveabaord is for everyone, but in my wide breadth of experience, I prefer the Nekton.
Just as you found the crew to be remarkable, give the ownership time to react... then post what you find out! I am sure they are pretty busy trying to resolve whatever problems stopped your adventure cold.
Please keep us posted as to the resolution of this matter, I have no doubt that you will be compensated in some fashion for missing what you came there for! Let us know how it works out for you.