Are they neutered? This makes the process go a lot more smoothly normally. If they are both entire, then she is probably already pregnant! If he is entire and she is neutered then he will probably continue to try and hump all the time and drive her crazy.
Sometimes, humping can be a dominance...
I am really glad you asked before going ahead with this, please, please do not get a guinea pig to put with your rabbit. I am actually amazed if any rescue centre would allow this pairing, he would be much better off with a female rabbit - nothing can beat companionship of the same species...
Take her to the vet. It may just be an eye infection that she will need drops for, or (as it is on one side only) it could be that a foreign body has got into her eye.