Welcome to the world of aluminum - as another former wood boat owner, I think you'll appreciate the advantages while you probably appreciated the 'classic lines' that make our boats popular with 'woodies'.
It sounds like the area you are writing about probably had a weak spot in the barrier coat. One of the ongoing debates on aluminum is this: if the hull has no paint whatsoever, charges are dissipated over such a broad area that they may lose most of the damaging effects. When the hull is painted, any small unprotected areas take the full hit and corrosion at those points is much greater.
We're in salty water on the Chesapeake Bay, so we have a professionally applied (by EPA license) barrier coat, then bottom paint. There are a lot of Marinettes on the bay and somehow they're still afloat. Fresh water is a lot less worrisome. Of course, never, ever, use any paint with copper anti-fouling, you'll create a great battery and the copper will win over aluminum every time.
As to the pitting, our boats have 3/16" hulls with 1/8" elsewhere, and some degree of loss is engineered in. A certain amount of pitting has occurred with most, if not all Marinettes to some degree. You'll get plenty of much better informed replies than this, but for my money, unless the pitting is really deep, get the barrier coat FULLY applied after blasting or sanding clean and you'll get many more years of pleasure out of your new boat. The key is, absolutely EVERY minute spot of below water hull must be coated, with no room for error. Use more than one coat, to ensure that what you missed the first time will get covered by subsequent coats.
Also, continue to follow all of the chatter on this site about our Capac monitoring system and galvanic isolators. Make sure you, your marina and your neighbors' boats do not have any leaking charges and you'll be fine.
You did not mention your sacrificial anodes. If they're okay, that could be good or bad. Ask the seller when they were last replaced. If they look good after any great length of time in the water they are probably not connected galvanically to the hull, so once again, the hull is the battery and your 'zincs' are nice ornaments. If they are badly corroded, replace them before you splash the boat. Marinette has the complete set of correct anodes available. Make darn sure you've abraded the points where the bolts pass through and use lock nuts that will dig into the aluminum when the bolts a drawn down.
As to getting through a season, that's a judgment call, but again, in fresh water you're probably okay. You could really hedge your bets if you did not plug in to shore power, but if so, you'd better make sure you run often enough to keep the batteries topped off. We have a 32' Sedan, with half the open cockpit you have and a camper cover that keeps it dry when at the dock, Therefore, very little trouble with water in the bilge. If yours has good covers, consider it, but listen to the folks who are going to jump in behind me on this one!
Enjoy your new boat, send some photos...
JIM
Alexandria, VA
1989 32' Sedan
'Gammelby'
Friendship, MD