Ride 'em. Depending on how often the tire rubs the chainstay will allow you to judge what's acceptable. Just check them after every ride. Sooner or later you won't bother because it doesn't happen or, it happens and you search for skinnier tires.
If you're really worried about marring the chainstays, then put some duct tape at the potential contact points and let it sit for a few months. If the tire rubs the tape, the chainstay is spared and you have your answer.
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