In the 3rd overtime, teams must "Go For 2" after scoring a touchdown. OK, but what if they don't?
There's your problem right there. There is no such rule in the NFHS Suggested overtime rules, so there is no MFHS interp. However, many states modify the NFHS procedure. For example, in Georgia, we start on the 15, not the 10, and you can get a first down without scoring.
If the state has put in the "must go for 2 in the 3rd overtime" rule, then the state needs to come up with the answer to your question. I would think the easiest thing would be to use the NCAA interp: go for one if you want, it just won't count for any points.
And yes, there could still be roughing the kicker, as it's a legal kick, it just won't be worth any points.