Sure. You can get a transplant after C-Diff, but probably not until the C-Diff has resolved.
Because the C-Diff lives in the gut and not the lungs, it wouldn't be "removed" with transplant (unlike, say, a mild PA infection in the lungs), so they wouldn't want to transplant you with an active C-Diff infection. I could be wrong though, and there may be exceptions. I know C-Diff is a fairly common pre- and post-tx complication for CFers, b/c it's typically caused by antibiotics (which deplete the good bacteria in your gut and allow the C-Diff to flourish). I've been treated for C-Diff before. It definitely doesn't disqualify you from a transplant.
By the way, typical treatment is with flagyl -- a nasty antibiotic that is nonetheless better than the infection! Good luck...in most cases C-Diff resolves without a many problems, I believe.