Or just change pens. You can find permanant markers in a fine tip, artist pens are sometimes waterproof once dry, and different pens are more/less waterproof - though it has been a while since I tested standard pens, and a ball point (or mechanical pencil) is much cheaper than the waterproof options.

I'd think that the bigger problem when leaving a journal in the rain is trying to keep the pages from sticking together as it dries. Probably a lesser problem with the coffee unless you have a major spill.