As I explained, what changed were the circumstances. In the past, heresy implied a whole lot more than it does in a society where religious unity in civil society is already destroyed. The same principles regarding the application of the death penalty applied then as it does now. This is from the section on the execution of criminals in the chapter on the commandment against killing in the Roman Catechism (aka Catechism of the Council of Trent) published not long after Exsurge Domine:
The end of the Commandment is the preservation and security of human life. Now the punishments inflicted by the civil authority, which is the legitimate avenger of crime, naturally tend to this end, since they give security to life by repressing outrage and violence.
This is the same reasoning in the modern CCC.
So yes, ask someone today if a heretic deserves death, and everyone would and should say no, since nowadays that just implies that you’re one of many people in an already pluralistic society who denies an article of faith. However, if you phrase it another way, like asking if someone who is attacking and threatening the very stability of society and putting the lives of many people at risk (not to mention souls), and other means to stop the person are ineffective, can putting that person to death be justified, then I bet a whole lot more people would agree that in such a situation death is justified. The only difference is people in the past, based on their experience, associated those factors with heresy whereas now it is not usually accompanied by those factors.
Again, as I mentioned, the experience in the past was that heresy tended to lead to such things if not repressed (just look at the chaotic and bloody aftermath of the Reformation itself and it’s no wonder St. Robert Bellarmine thought it was a good idea). But, since that violence has died down, we’ve learned to co-exist peacefully for the most part and so we no longer see it as being justified (although, there are analogous situations in modern times, like when the US government went after the Branch Davidians or what’s going on with ISIS in the Islamic world).
To me, this issue is no different than two people applying the same just war doctrine and coming to different conclusions about a particular war, especially when one has more factual knowledge and experience than the other. We may look back with perfect hindsight and say a particular war wasn’t justified after all, whereas the people waging it at the time may have been doing so in good faith based on the information they had.