Sorry to hear this, I can't even imagine how aggravating stupid things like this are

Are the handle and lock still functioning correctly? The clips/mounts behind the handle that connect it to the body may have been damaged, and might not be able to go back into place then.

As for the rest, I would say your best bet is spending a few dollars on some touch up paint, and you'd be able to make it look 90% better.

If you need to buy a new handle, it would come in unpainted black plastic, so you'd need to find a way to get it painted then

 

The handle and lock work fine, and it's not loose. If there were some kind of putty or fill I could put in the small holes and touch up paint over it'd be ideal, but maybe that'd make a mess inside. If you have any suggestions I'd appreciate it. Also if there's a particular touch up paint that's given you good results, let me know where to get it. Thanks, TG!

 

Buy touch up paint from the dealer. It will be closest match. I think it usually runs less than $20 for a little bottle.

 

You could try using this as body filler

http://www.amazon.com/dp/B0007ZG9TO...t_dp_o_pd_nS_ttl?_encoding=UTF8&colid=3UYZDK56PQNQP&coliid=I1NNVSQ5CMGIYK&psc=1

Here's a website that sells Jeep paints, check to see if they have your color.
MOPAR 82400891 - MOPAR® Touch Up Paint 5 oz Spray Can - Quadratec

Getting touch up paint from the dealer would work just as well, whatever your preference is. As long as it's official mopar paint it should match very well

 

Once the metal is exposed you will risk rust
A little filler and touch up paint should be fine
You should try to remove the handle, clean/prep the edges then fill and paint
Short haired filler is fine for such a small spot
Usually when doing so you extend past the area but for this would keep it minimal
As close to only where needed as possible