I personally would worry more about the damage the water has done by sitting in there for so long than a little water in the oiling system.

We have to deal with a similar situation at my dealership on an almost daily basis. When replacing timing chains on the cadillac 3.6l you have to remove the front cover, which has coolant passages going through it for the water pump. When you first crack the seal and move the cover back, you hear about a gallon of coolant rush into the oil pan. No way around it. I just let the coolant drain as long as I can, then just refill with oil when the job is done.

Unless an engine has been ran with a large amount of water in it, your not going to have bearing problems. Waters not going to wash out your bearings unless its pumped through the oil pump. So Id change the oil, run the snot out of it, and maybe change it again to get the moisture out and call it good.