I don't think long rests should be punished necessarily, but one way of limiting them could be to just increase the number of short rests you get and then have it be that you can't long rest until you've used up all your short rests. Sure someone can just spam short rests and then long rest, but it's far harder to limit long rests in a game like this given there's no real timekeeping mechanic internally and there's no real way to limit how many combats a player will get into between long rests nor how deadly those combats will be.
