The text is very clear, despite differences in nusach. Vechol hakinim(heretics) cerega yovaydu, means they will be destroyed. Al tehi sikva, they should have no hope – no hope for anything. They have forfeited all of their connection to klal yisroel by their egregious sin of heresy.
If they do teshuva, fine, but we daven for their immediate (kerega) destruction. Tell me, would you daven for a kapo to do teshuva? What about a nazi who happened to be Jewish? Davening for teshuva has its limits, and chazal place those limits squarely on apikorsim. Reshoim who are full to busting in sins, we daven for. Heretics we don’t. I’ll look up your quotes from rav yaakov emden and such, but the text is rochel bitcha hakatana clear.