Daas,
I was unaware of that Gemara. I don’t recall ever seeing that we are kofin on mitzvos eseh. I will look into it and get back to you.
Mdd,
I know that is the stam assumption. I understood that Gemara to be saying that if the Bais Din sees a problem spreading in the otherwise frum community, then they can declare horaas sha and execute somehow outside of the Torah’s normal requirements. The purpose is to shock the rest of the population back into proper observance. But if you are dealing with a population that is completely frei, executing a person for turning on a light on shabbos will create anger and possibly violence from the rest of the population.
At a certain point things are so bad that executing doesn’t help and if doesn’t help then it is just murder, plain and simple.