Another possibility is to use transformers on your AC coming out of the generator. If you step down each phase (that's 3 transformers for 3 phase) before rectifying, you don't have to worry about doing AC/DC conversions afterwards.
Of course it would be awesome to rewire your stator if it's such that you can do that. For example if each phase has 3 coils in series, you could just rewire them in parallel and get 16V at the same RPM as you got 48V with them in series. (Possibly introducing other issues, but the more experienced folks can help me with that.)
Or if you stator is in star, you could rewire it for delta and get ~28V.
I'll agree with Roamer that if you center-tap your battery banks... and center tap your center-taps, you'll have all kinds of weird issues, unless you have some way of making sure you draw power equally from each cell... which is nearly impossible.
The only thing I can think of is if you completely cycle each battery on a schedule. Which would be inconvenient and impossible to do if it's not automated... but if you 48V bank starts at 0% DOD, then you go into "load mode" and put your 12V inverter on the first battery until it's down to 20% DOD. Then move on to the second, third, and fourth. When all four batteries are down to 20% DOD then you have the option of going back to "charge mode" and hook the whole 48V to the genny, or go back to round-robin discharging each battery. But you'll really want each battery to be at the same level before you start treating them as one in series.
I'll be watching this thread closely, because I'm incrementally building my setup very cheaply, and I expect to start introducing some mismatched components at some point or another.
My instinct: 12V inverters are a dime a dozen, so you shouldn't have invested too much here. Sell it, and buy a 24V unit. Try to get your genny producing 24V (or take the hit in amps and let your batteries pull it down), and configure your battery bank for 24V. You won't be at 100% efficiency, but it sounds like you (like me!) will be happy if it works at all, and it will.