So far, you've just said that you feel guilty about not wanting sex and that he feels rejected, but it's not really clear from your posts whether you've really talked to him properly about this other than some vague hints about 'gynae issues' and having a toddler. Have you actually sat down and explained really clearly how physically uncomfortable it is, and how you bleed for days each time and that's quite debilitating as well as being a nuisance? You say that there's plenty of affection and that you have a good relationship, so I think you need to put your guilty feelings aside and have a proper talk with him.
He is obviously attracted to you and has a sex drive, so of course, he will inevitably feel sad at the prospect of what could potentially be a long time without sex. I don't think you could expect anyone (male or female) who had a reasonable sex drive and a loving relationship to be delighted at a sexless relationship.
But you can explain to him that you do still fancy and you do still love him (I assume you do?!) and that this isn't about you rejecting him, but is purely about your physical/hormonal problems that are making sex really uncomfortable and a bit scary right now. If I were in his shoes, I would feel a lot better about being turned down if I was fully aware of exactly why it was happening.
I do think, though, that you absolutely should not fall into the trap of thinking it can be like this forever, or doing nothing to remedy it. Hopefully, your physical health issues can be addressed, but you might find that even then, there are psychological barriers for you, and that you might need to do some work (whether it's therapy or counselling or whatever) on re-establishing a sexual relationship. And that's for your sake as much as his - you deserve to have a sex life too.