Given the Caretaker literally abducted people and conducted experiments on them, I doubt he'd have much of a moral high ground when it came to judging the Equinox crew. Besides, in the even they did do anything the Caretaker found repugnant, it's basically his fault anyway since he's the one who put them in that position to begin with.My guess is that some combination of Ransom, Burke, and other Equinox crewmembers tried something morally questionable, resulting in the Caretaker booting them away.
Kes was the only Ocampan in that solar system not living in their settlement. Pretty sure she didn't have any run-ins with the Equinox.I suspect the crime had something to do with how they treated an Ocampan refugee or something along those lines.