We've booked our own & used the cruiseline dives on our cruises to Cozumel. There would have to be some very unusual circumstances to cause you to miss departure if you were to book dives on your own. many of the cruiselines use AquaWorld, so you would be on a large boat with 16 - 24 other divers. Even though they split you up into groups of 8, with a DM, that's still a lot of people going into the water in a short period of time. It will also take up more of your time on the island, limiting what you may be able to do after diving.
If you don't get to dive, and want to spend some time snorkeling with your wife, I would suggest catching a cab and going to Corona Beach. Good snorkeling, easy access, cold beer, good margaritas & decent food. Main thing, you wouldn't be surrounded by tons of people....you'll probably be ready to see fewer crowds as you'll likely be spending the week with a minimum of 2000 others. Spend a few hours there & then head into San Miguel for some sightseeing & shopping before having to head back to the ship.
Main thing.....have fun while you're there!
Mike