“One of the main topics stirred up by the Slifkin affair was the binding nature of Agadda. He, and many others, quote several Rambams in Pirush haMishnayos, which they understand to mean that he won’t pasken divrei Agada. Of course, in Yad HaChazaka he paskens several of those same issues…”
Why are we assuming that the fact that something is written in Yad HaChazaka makes it a “psak”? All it means is that the Rambam feels it to be true. In fact the Tosfos Yom Tov [on the Mishnah in Sotah(3:5)where the Rambam says that he doesn’t pasken these types of things] says exactly what I just said, to answer why the Rambam brought down Rebbe’s position in the Yad HaChazaka.
“The basic problem with the position is that it is very halachically significant to know if someone is a kofer/min etc, and that depends if their beliefs are correct – but the issues of correct beliefs are (mostly) Agada!”
Just because the Rambam couldn’t “pasken” what the correct beliefs are doesn’t mean that he couldn’t determine what they are, and thereby determine who is a heretic.