While I understand the concerns about her health while staying with you, and even agree that perhaps it's better he is at hers as she is so unwell, I am not sure it's as simple as "discourage the relationship" as some PPs have said.
Sixteen years olds aren't twelve year olds. While most teenage relationships don't last, I do know lots of couples including my parents and my brother who met their partners at that age and are still together, married, kids, grandkids etc.
At 17 I was definitely in love with my boyfriend. It was an actual relationship - not a child's version of one. I wasn't very mature, and neither was he, which probably contributed to us breaking up but my feelings were not of a child with a silly crush.
I feel like trying to get them to split up is going to send them all Romeo and Juliet and "us against the world". Your DS is going to think that you're horrible to tell him that he should break up with his gf because she's unwell.
I feel like all you'll do is push them closer together and make him want to speak with you about it less. Then if he actually does start having doubts and wanting to leave her, he'll be less likely to speak with you about it and even feel like he has to keep going as he doesn't want an "I told you so".
I feel like the cleverest thing, if you think your child's relationship isn't particularly a good idea is always to be extremely supportive, be kind to the partner and be a person they can confide in.
Maybe you can speak with the parents or maybe there's a charity you can get general advice from. If medically it's a bad idea for her to be with you so much than you can discuss it from that angle. But I'd really think that it will be much more successful if you come at it from a place of care for her.