a : dissent or deviation from a dominant theory, opinion, or practice
b : an opinion, doctrine, or practice contrary to the truth or to generally accepted beliefs or standards
So, you can have a "scientific heresy", "political heresy", "social heresy", or even "40k list building heresy". It does not require acceptance of the Emperor as deity.
On the subject of the recent retcon, a number of people flinched and said they could "see that" BT might venerate those who had "touched the Emperor" (sanctioned psykers). I thought about agreeing, it kinda, sorta sounded reasonable, but something kept stopping me from doing so, even though I remember arguing that since the Emperor had sanctioned Navigators and Astropaths, the Black Templar would accept them, so it wasn't that big a deal, right? I found the answer in some of my recreational reading. It goes a bit, you have been warned.