Its probably the most annoying design flaw with these trucks. I have had to shut off the truck a few times to rinse the alternator out. Sometimes it works, other times... thats why I carry a spare alternator!
Not much you can do about it. The OEM Toyota alternators hold up better then the aftermarket ones, but are still a critical point of failure on these trucks. Carry a spare, run dual batteries, and be careful when charging into those mud / water holes.
This crossing cost me an alternator:
These ones didn't:
I don't really have a list of do's and don'ts together, but generally watch your speed going into deep mud or water, and if you get in really deep stuff, put a tarp or blanket across the front of the truck to try to keep as much out of the engine bay as you can...
Hope this helps.