Eh, that's not a bad idea, but I wouldn't want the park to waste money retheming a perfectly fine ride. I'd rather see them use the money to add on to what little theming there already is, plus use the bulk of it to add tons more effects to get people soaked. The year after the ride first opened, there was a proposed plan to add a tunnel and other water effects to ensure everyone got soaked, but it never happened. I say, harken back to these plans and add that tunnel. Also, we could add some scenery, similar to what can be found along the Jungle Cruise, like cheap animal animatronics and angry natives. A soundtrack of suspensful, tribal music could be playing. The station building could be rethemed like the Jaws ride at Universal, with some sort of "boat tour" theme. It could be a fictional cheapo Congo boat tour company, with humorous signs along the queue like "Congo Jack's Tours is not responsible for patrons thrown out of or ejected from the boat or eaten by piranhas or hippos".
I think the public would like this "on the verge of danger" theme a lot, it would attract people more than Looney Tunes. And besides, nothing looks worse than when a colorful ride or area gets neglected and faded. Like what's probably going to happen to Wiggles World in ten years.
Especially since the ride is alreadly supposed to have that theme considering the current unload spiel goes along the lines of "Welcome back riders, it seems like you all survived the perilous trip through the rapids of Congo Rapids". Too bad you can't hear it at all since it's only played through the speaker on the near station next to the op booth.
Anyway, with Weber in charge now and the 50th anniversary coming up I think there's a chance we will get some sort of upgrade, even if it's just a matter of turning on older effects.
EDIT: Also earlier from Nitro's lift you could see someone in a truck with a cherry picker bucket on it doing something on the top of the rock wall at the final turn of Congo just before you enter the station. Where one of the waterfalls used to be I believe. Maybe this is a sign of the ride being upgraded, at least from its current state.