From The Phantom Edit onwards most editors have removed the sea monsters from TPM arguing with validity that in the context of the scene they did nothing and the sequence was little more than an effects showreel.

What if Jar-Jar was redubbed and instead of being worried about what his own people would do to him and his new Jedi friends he was instead worried about the creatures that the Gungans use as natural protection for their city?

That way when Jar-Jar and the Jedi dive to the Gungan city they could menaced by the creatures without even the limited protection of the sub and the creatures would serve a story purpose.

Naturally it would require a lot of editing and creating new shots by scaling down existing shots of the trio diving and swimming (and using CGI and/or actors for wide shots) so it would not be an easy idea to use but it would preserve some of what Lucas had in mind while giving it tangible story value.

The Gungans could call off the attack themselves and allow them free passage past the creatures after they have been given the sub.

Adding a lake to the Gungan battle field could give the Gungans the opportunity to call one of these creatures during their battle with the droids adding extra value to their existence in the story.