I don't think you have a choice. If you leave the goop on the good eggs they are going to most likely be contaminated and not hatch anyway. I would wash them gently with warm water and then pat dry with paper towel.
I've had to wash off some because of breakage in shipping. Sometimes they do go ahead and hatch and other times they were just handled too roughly and still don't hatch. I've gotten lots better at checking for broken air cells though since I first started. Those with the broken air cells still are very unlikely to hatch even if you do clean them.
Hold the egg under warm running water and gently rub with your hand. then wipe dry. Make sure all the egg residue is off or it will block the poors. Make sure you do not jostle the eggs while washing or drying, sounds like they have had a rough trip. If the eggs are viable, hatchability should not be affected too much. good luck!