With a good belt like the goodyear gator back, and at correct tension you shouldn't have any squeal when going through water. Remember these jeeps (at least the 4.0's) seem to require a higher than normal belt tension compared to other cars/trucks. Even when you think the belt is tensioned tight enough many times when the a/c compressor kicks on you will hear belt squeal or if you rev it fast. which means it needs a tighter tension.
as for the water on the brakes not much you can do about that, except as suggested above, ride the brakes right before you hit it and after for a little bit. I would not try to install those brake dust cover type sheilds you see on some BMW's and such, they reduce air flow to the brakes, look terrible and can cause more problems than they cure IMO.
Take note that some brake pads seem much more prone to terrible wet rotor braking than others. i had a set of pads on one of my cars one time, that was SCARY with basically no braking when the brakes got wet, yet otherwise performed great.
THough i typically suggest and use myself, plain brake rotors, the slotted or drilled rotors will help get that rotor to shed water/mud faster, especially so for the slotted.
If i was you, i'd throw on a good year gator back and tension it good and tight, and change your brake pads for something else (i run the PFC's (performance friction compound) from autozone and they work very good (wet braking and otherwise), and are a brand that autozone carries, not 'their' brand.