Salt water that is trapped in the lines for a few days will give you a hydrogen disulphide smell but it will come and go in seconds - it does not linger. And as has been already posted, if you're living aboard and using the head regularly it won't smell at all.
The smell you're worried about is IMHO definitely not worth replumbing the head to fresh water. Eventually you're going to want to sail overnight or longer then you won't have the marina fawcet to rely on.
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