Not too much to do in San Miguel, but it's safe and easy to walk/shop. Many days there are hoards of cruise shippers everywhere. Like being at the Minnesota state fair!
Find out where your Dive op does it's surface interval, (many do intervals at beach day-resorts) such as Mr. Sancho's
http://www.mrsanchos.com/, your wife could grab a cab from the plaza after she's seen it all, and meet you for lunch then hang at the beach, get a massage, swim, snorkel, horseback, jet ski, etc. while you make your second dive. Your Dive op might drop you there after diving, then you could grab a shower, the wife and cab and head for the un-developed east side for a drink or meal on the beach at one of the few beach bars over there. You will circle the island and close the loop at the ferry dock.