We joke, but Epstein masqueraded as a wealthy investor/entrepreneur for like two or three decades before he was caught, so him merely having some one's contact written down doesn't mean much. In fact, Bill Gates has never been shown to have visited the island at any point, and Epstein was very invested in the Gates Foundation charity work such as loaning his plane for high profile individuals to fly to charity sites across Africa.
While I thought the same at the time, since then I've adopted a more nuanced view. My guess is that she was planning to divorce him for a while and just used an opportune moment to actually do it. Some rumors that can be explained away are not something that would end a healthy marriage.
I always thought it was more to do with the fact that their youngest son had just turned 18. So he was probably moving out of the house to college. There is a big culture here in the US to "stick it out for the kids until they move out" mentality. So I just thought that is what they were doing.
There's evidence that Gates knew what was going on at Epstein's parties, didn't participate, but still choose to stay silent. Gates had enough power and wealth that he didn't need to worry about retaliation either.