Two things, ditching a rocket into a bath of salt water is probably as bad as it is for a combustion engine in your car. Perhaps a giant water tight rocket condom would do the trick along with something to slow the fucker down so the impact with the water doesn't hurt anything. Unbuilding/rebuilding such a rocket is probably more of a waste of time than building a new one. Because when you build one from scratch there are built in safeties and quality at every single step, nothing has been used. Every water logged rocket would clearly have different problems, but how complicated is the cleaning process?
Second, "Assuredly losing the vehicle to bad sea swells" is clearly not the case. Did you watch the last landing? That thing was dead center, which means the barge and the rocket were both in precisely the right place. Stabilizing the barge to absorb the impact, making the barge capable of having a near motionless deck in obscene seas, these are all possible solutions that you seem to think are impossible to solve. Just because there are 13 foot seas, doesn't mean the barge deck is pitching like a crab boat.