First of all, GI Jane is a movie. It was directed by Ridley Scott, who also directed Blacck Hawk Down. The major difference between the two movies, besides some 6 or 7 years, has to do with Pentagon support. Whereas BHD had full Pentagon support from aviation resources down to military advisors that were actually in Somalia, GI Jane had minimal if any support. Anyone who has watched The Discovery Channel in the last couple of years has seen their documentaries on SEAL training. Compare that footage to that of GI Jane and you'll see a difference between night and day: the real world vs. Hollyworld. Pay attention to the facilitlies as well. The best point I can make is the aircraft used in either movie. BHD had real Blackhawks and Little Birds. GI Jane used neutered rental AH-1S Bell Cobra attack helicopters and repainted HH-3 Sikorsky Coast Guard rescue helos.
Second there is a field technique for protecting the rifles during water crossings described in one of the government manuals. It entails using a shoot off plastic muzzle cap over the flash hider and keeping a round in the chamber.
You have to remember that the rifles issued to troops in the field are working rifles and not the pride and joy of a civilian collector. As such, they're going to be used and abused
(Due to the small bore and high velocity of the bullet, any obstruction in the barrel can be dangerous.)
Unless you have imminent contact that requires return fire, you remove the cap and with the muzzle pointed down, break the seal at the chamber end by pulling the charging handle back slightly, but not far enough back to eject the round or cause a double feed. This allow water to run out the muzzle. Water in the action and buffer tube will drain out the trigger openning.
When time permits, the rifle should be field stripped, cleaned and lubricated.
After the mission or patrol, the rifle will probably be returned to the unit armorer for a more thorough inspection and cleaning. The rifle is repaired or replaced as necessary.
Condoms are better suited for their intended purpose. Shoot through water proof bags are probably noisy to handle plastic, are useless after that shot and are probably a pain in the ass to get open to remove the rifle.