That dictionary entry sounds to me like it's being deliberately broad and vague to step around the endless flamewar of some religious arguments, so I'm going to offer my own more specific definition and a bit of associated speculation and context, at risk of starting an argument. The term "heresy" is Christian in origin, and is/was loosely part of a set of terms:
1.
Schism is when two Christian churches differ over a small but irreconcilable point, though what is "small" is itself a source of much discourse, and the point of difference is usually outside the core doctrines. A classic example of Schism is when Church A thinks the Papal Election of [year] was illegitimate due to the military occupation at the time influencing the outcome so they follow the other guy who was picked to be Pope in the do-over of [year+2], whereas Church B thinks the [year] election was irregular but valid because the military occupation did not directly compel the vote so they're with the [year] Pope and the [year+2] guy is a pretender, what's illegitimate is holding an election when there's already a Pope. The two churches still agree on the substance of what one should believe about Christ.
2.
Heresy is when two Christian churches disagree over a larger point of Christian doctrine, for example whether Jesus existed from the beginning of the world and was only waiting to incarnate on Earth, or whether Jesus was created at the moment when Mary conceived. The mainstream Christian creed teaches the former ("we believe in one Lord Jesus Christ, the only begotten Son of God, begotten from the Father before all times") and would therefore regard the latter as heresy, and vice versa. Generally, if it's a disagreement about Jesus but both churches still believe in Jesus, it's heresy.
3.
Heathenry is how a Christian describes someone who doesn't believe in the Christian God at all, and/or someone who believes in other deities. Sometimes you'll see this split into "atheist" and "pagan", and sometimes "heathen" is used to describe the latter only, not including atheists.
The substitution of another church for Christians in interpreting the word is straightforward. Beyond that... well, Warhammer Fantasy includes some weird quasi-monotheist cults believing e.g. that all the other gods are secretly Ranald in disguise, but nothing like the RL monotheism that gave us the word "heresy". Also, I practically never see "heathenry" used in WHF. So between the official polytheism, the limited vocabulary, and my general observations of WHF, I think the use of "heresy" in-setting mostly covers something like #3, being a cultist of forbidden gods and/or denying the Imperial pantheon, and #2 to a greatly reduced extent, given the degree and number of divergent splinter sects in canon that are not considered heretics.
*shakes fist at GW* (note: the official Cult of X sometimes declares a sect of X to be heretical, like the Sons of Ulric, so there's at least some #2 in the WHF definition.)
Games Workshop is evidently doing some of their usual weird nonsense where they co-opt a cool-sounding term and implicitly redefine it for their setting without spelling out its new meaning properly, because in addition to the above, there's item 7 of the Imperial Articles of Magic: Whoever studies necromancy is a Heretic. The lores of the Chaos Gods are heresy, sure, that one makes a kind of sense. But
necromancy? What?
Other canon points of interest:
There were times when the Ulricans believed all the early Sigmarites were heretics. I'm guessing because Sigmar wasn't yet an approved god.
There's a miscast entry named
Heretical Vision: "A Daemon Prince shows you a vision of Chaos. You gain 1d10 Insanity Points. Any time after this event, you can spend 100 xp and gain the Dark Lore (Chaos) talent."
Your mention of [arcane] Magic as an example of no-longer-heresy was not merely illegal, but believed to be associated with the Chaos Gods. In particular, Tzeentch, who is kinda-sorta the God of Magic, and the wizard miscast rules are sometimes named "Tzeentch's Curse" in the rulebooks.
Witch Hunters are tasked with searching out heretics, though Realms of Sorcery says their scope does
not include "traitors, seditionists, or revolutionaries", which suggests there's a religious component required to be a heretic, not merely being at odds with what's generally accepted. OTOH, Witch Hunters are also tasked with hunting out, again, necromancers.
Something funky is going on with necromancy that gets it included into the WHF definition of "heresy" repeatedly.
