Right. Putting them and Kirk on the same level and giving Kirk the advantage. I would assume a Jedi would be able to tap into the force, even if it was different in a new galaxy vs his home galaxy, but Kirk would have the advantage of knowledge for an immediate battle. A Jedi could potentially counter many of the technological weapons Kirk would have at his disposal, but the element of surprise and his general sense of tenacity when it comes to finding the weaknesses in his enemies would be Kirk's battle if it were immediate. With training and time, the Jedi would overpower Kirk. The Jedi won't know how the ships and teleportation work immediately.. but with training, sure.Though in my experience with crossover battles, you always presume characters have access to their strongest features - people like using Master Chief from Halo, and it's usually implied he has access to MJOLNIR. Same with Kratos, it is just implied he has his chain blades. A Jedi without the force or a lightsaber, he's nothing more than a finely trained spec ops soldier.
If Kirk were going into their galaxy, being trained to have to deal with anything being thrown his way, I think that teleportation would still be his key ability in survival against a Jedi attacking him as it would still take the Jedi by surprise--most people just do not teleport in that galaxy. I think Kirk could rid a Jedi of his light saber, but the force itself would still make the Jedi the victor as Kirk has no real weapon against it. It is everywhere. (Now Spock, on the other hand, may be a victor if he could get his hands on the opponent and do that Vulcan pass-tfo trick.)