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My instinct is telling me it would be good to just let him know this and that I think it would be better to try to become friends,
I think you can go with your instinct on this; tell him that you are not feeling well enough to go out. But I would not tell him that you'd like to become friends. Logically, if you are not well enough to go out on a dates, how are you well enough to do something together with a friend? Also, to guys, being friend-zoned is loathsome.
It's possible to simply become friends without asking; "Can't we just be friends?" It's done by keeping an open line of communication.