I have a daughter with IBD but she's a young adult. She had to choose between going to school virtually last year or being on campus (though most classes were still virtual). For the fall semester, everyone was virtual, so that wasn't hard. The spring semester was harder because some of her friends were back on campus and she was a senior but both her GI and rheumatologist did not think she should go back to school in-person. And she did understand this because she knew how sick she could get if she got COVID. Virtual school actually ended up being beneficial for her because she was in pretty bad shape during the spring semester (IBD flared and so did her arthritis). So being at home actually helped her.
As a high school teacher, I used to really think that kids missed out on a lot if they were doing online school. And I still do think that - extracurriculars, physically seeing and interacting with their friends daily, playing a sport and being on a team, volunteering, working in groups and having class discussions, traditions like prom and homecoming etc. Both my daughters did homebound school for a short period of time due to flares. They absolutely hated it - missed their friends and missed going to school.
But in certain situations, virtual school makes a LOT of sense. Having a 5 year old with what sounds like pretty severe IBD would definitely make me consider keeping her home during a pandemic, especially since she is too young to be vaccinated. I know from my colleagues that they put a lot of time and effort into making virtual school like in-person school in terms of academics. But I used to teach high school and your kiddo is a lot younger. And I do know that virtual school is a LOT harder with very young kids.
But virtual school won't be forever. Whether you choose to enroll her in virtual school or to homeschool her, at some point she will get vaccinated and hopefully be able to attend in-person school. And honestly, even if she misses some part of kindergarten, she is going to be just fine. I would try and see if you can find a way for her to meet other kids - it could be a sport like soccer or softball or gymnastics or dance or anything that she's interested in where she gets to meet other kids. An outdoor sport like soccer is probably safest (but my daughters both played soccer starting at 5 or 6 so I'm biased!!). But really, any activity works. You can also form a "pod" with other families so that each family shares supervising virtual school and their kids get to meet and play with other kids.
There are may options. Your GI can also advise you - I'd reach out to him/her. Good luck!!