The only way you can make it work is to re-dub Jar-Jar's lines so he doesn't sound like Stepin Fetchit.
Ideally I'd keep him as an African American voice but an intelligent one to really flip the character around.
Intelligent people can still be clumsy (think the tweedy professor archetype).
Turn him into a Gungan Rupert Giles without the accent and you would be onto a winner.
This would give you opportunities to also write better lines which would make the character more interesting.
EXT. NABOO SWAMP - TWILIGHT
QUI-GON runs through the strange landscape, glancing back to see the
monstrous troop transports, emerging from the mist. Animals begin to run
past him in a panic.
One of the huge MTT's bears down on the JEDI like a
charging locomotive. An odd, frog-like Gungan, JAR JAR BINKS stands transfixed until he spots the escaping knight.
JAR JAR : Oh my! You there, get Down!
JAR JAR and grabs onto QUI-GON as he passes. The JEDI is
caught by surprise.
JAR JAR : (Cont'd) Let it pass over you it's your only chance of survival.
QUI-GON : Let go!
The machine is about to crush them as QUI-GON drags JAR JAR behind him. Just
as the transport is about to hit them, QUI-GON drops, and JAR JAR goes splat
into the mud with him. The transport races overhead.
QUI-GON and JAR JAR pull themselves out of the mud. They stand watching the
war machine dissapear into the mist. JAR JAR grabs QUI-GON and hugs him.
JAR JAR : Are you alright I'm sorry I had to resort to...
QUI-GON : Are you brainless? You almost got us killed!
JAR JAR : I'm considered intelligent, I speak for the Gungan council.
QUI-GON : The ability to speak does not make you intelligent. Now get outta
here!
QUI-GON starts to move off, and JAR JAR follows.
JAR JAR : It's a very dangerous situation you look like you need assistance.
QUI-GON : That wont be necessary.
JAR JAR : It's not a cultural tradition of my people to try to be helpful to strangers but...
In the distance, two STAPS burst out of the mist at high speed, chasing
OBI-WAN.
QUI-GON : I have no time for this now...
JAR JAR : .you really have awful manners.
The two STAPS barrell down on OBI-WAN.
JAR JAR : (cont'd) Take cover!
QUI-GON throws JAR JAR into the mud.
QUI-GON : Stay down!
His head pops up.
JAR JAR : I see. if I do it I'm brainless, not that I'm ungrateful of course but...
The two troops fire laser bolts at OBI-WAN. QUI-GON deflects the bolts back,
and the STAPS blow up. One-two. OBI-WAN is exhausted and tries to catch his
breath.
JAR JAR : Is this your friend?
OBI-WAN : What's this?
QUI-GON : A local. Let's go, before more of those droids show up.
JAR JAR : They are not friends of yours I take it??!?
OBI-WAN and QUI-GON start to run. JAR JAR tries to keep up.
JAR JAR : (cont'd) It's all rather exhausting, I'm more of a swimmer, I'm not used to running, You'd be much safer in our city if I could...
They all stop.
QUI-GON : A city! (JAR JAR nods his head) Can you take us there?
JAR JAR : On second thoughts it's probably not a good idea, no.
QUI-GON : No??!
JAR JAR : They are a very insular people, they don't like outsiders much, My ambassadorial role has made me a bit of pariah to be honest. They may do terrible things to you if I were to bring you there uninvited.
A PULSATING SOUND is heard in the distance.
QUI-GON : You hear that?
JAR JAR shakes his head yes.
QUI-GON : (cont'd) That's the sound of a thousand terrible things heading
this way...
OBI-WAN : When they find us, they will crush us, grind us into little
pieces, then blast us into oblivion!
JAR JAR : He is very melodramatic but persuasive. This way!
JAR JAR turns and runs into the swamp.
EXT. NABOO SWAMP LAKE - TWILIGHT
QUI-GON, OBI-WAN and JAR JAR run into a murky lake and stop as JAR JAR tries
to catch his breath. The TRANSPORTS ARE HEARD in the distance.
QUI-GON : Much farther?
JAR JAR : This lake leads to the city, it's quite deep.
QUI-GON and OBI-WAN pull out small capsule from their utility belts that
turn into breathing masks.
JAR JAR : (cont'd) Are you sure I can't change your mind? The water will be warmer than the welcome..
OBI-WAN : Don't worry, this has not been our day for warm welcomes.
JAR JAR dives into the
water.
Breath masks on, QUI-GON and OBI-WAN wade in after him.