Really it was quite the high school drama. FINALLY a girlfriend and then she is making eyes at the guy with the fast car.
Kes was just friendly, there was really no indication she had ANY interest in Tom beyond that random future episode where they got married. She told Neelix she wanted to have his baby. That's a big deal for Ocampa being they can only have kids once. And that wasn't good enough, it didn't stop his obsessive behavior.
Sure the space dumpster driver is probably the most exciting man Kes had ever met. Of course all she had were other Ocampa who eat paste from dispensers and watch videos of the sunrise all day, and the Kazon who can't even figure out how to get water.
Ocampa are also said to mate for life. So it's really telling when Kes didn't backtrack on her possessed self dumping Neelix. She might have needed a nudge, but she realized after the fact was done it was the right decision.