Yes you can just install a 100 top end, including the cylinder, piston and head.
The kx 85 and 100 top ends are interchangeable so its quite possible that someone has installed an 85 top end on your 100.
You've got a couple options from here. Given that the cylinder is damaged and will need to be replated I would give Eric Gorr at Forward Motion Racing a call and do one of two things. You could have your head enlarged (assuming its not a 100 head on a 85 cylinder) and the cylinder bored to 100cc specs and replated, Your second option would be to purchase one already done. Check out Eric's garage sale items. He typically has 100cc cylinders ready to go. There are others that can do the same job but I haven't seen anyone with more reasonable prices or better service.
Complete KX100 top ends are typically in the $400 range form Eric and come ported to suit your preference.