I do research on infectious diseases in my day job.
To me this sounds like norovirus. As others have said, it doesn't discriminate with respect to its host. It has evolved to infect and then cause severe vomiting so it can spread itself to the next host.
Usually the body clears the infection pretty quickly, 1-2 weeks at most. Collins has been out longer than that but I doubt he is still infected. The problems for Collins specifically are loss of strength and dehydration which can last longer than the infection, and is probably a primary reason he hasn't come back.
The larger problem is the possibility of noro spreading to other team members. An individual may have no symptoms of a norovirus infection but could still shed the virus asymptomatically for weeks. This is incredibly serious for the success of the team this year and is absolutely a reason to keep Collins out for as long as possible. Team doctors can detect whether he is still shedding virus and shouldn't let him around anyone as long as that is the case. Obviously we can't have anyone else suffer from this, so we should err on the side of caution as much as possible. Our current playoff seeding certainly helps give us this luxury. Here's an abstract (many other similar out there too) talking about this sort of thing.
Shedding of norovirus in symptomatic and asymptomatic infections. - PubMed - NCBI
Like others have said, sending Rufus Johnson to IR could just be a case of needing that roster spot and not knowing how long he'll be infectious. Collins is critical to our success, so they're going to take different measures with him.
A couple other things: "Stomach bug" is a catch-all term that often means norovirus if it's a viral bug, but could be bacterial if it's from food poisoning (see Chipoltle recently). If this were MRSA it'd be extremely hard to hide it from the media, look at what happened to Tampa Bay a couple years ago; that was a huge deal.