Possibly. I've had a fair bit of success handling problems like this by carefully removing the case and allowing it to dry for 2-3 days. Overheating is an overcurrent problem, so the chances are pretty good that this will work.
Your chances can be noticeably improved by removing the battery and washing out the rest using deionized water (available at grocery/health food stores and major pharmacies). This will help remove any contamination from the water in the toilet.
Case removal directions: iPod Classic Battery Replacement
The reason I suggest deionized water: The existing contamination is water soluble. It may not be alcohol soluble. If you want to try alcohol, do it after a few good flushes with deionized water, since that will handle salt contamination. Alcohol is great for helping you get the last of the water out.