Its not the fact that it would only be on for a little while that causes the issues, its primarily the gas storage, even if its only in the tank on the generator, the fumes will seek the lowest part of the boat, from which there is no escape. Eventually , enough can build up to where a flash can occur.
If you wanted to add a generator, you could add a proper marine diesel genset if you have the room, course , not cheap.
I'd definetly replace the batteries, possibly increasing the house bank size. 8Ds are normal in marine applications, but you can do better, 6 volt deep cycles in series/parralel etc.
You coul also add a 3 rd bank, though it if you use shore power (AC plug in at dock) to charge your batteries, you would need a 3 bank charger, 3 way combiner.
A side note on most marine battery chargers (my 3 stage Xantrex included), they are notorious for boiling off batteries over a period of time, you MUST check the fluid levels in the cells of the bats periodically, 3-4 mionths is a good interval.
All in all you have everything you need already (except new bats). If you continue to plan for contigencies, well , you're going to be out of pocke a lot $$. A lot of this is already built into the system that you have, you just need to pay attention to it and maintain it.
I mean if you add a generator, ok what if the engine goes out, hmm maybe need another one as backup (actually one with alternator may not be a bad idea) ...