I can play Mata with religious characters of various flavours. It really is the "enslaving my people" that's the social killer. That applies to Angels and Sansha as well as Amarrians who support their empire.
This is actually a good self-test of whether the character's issue with amarr is a matter of religious culture or the whole slavery part.
A Vherokior/Gallente Angel vs. a True Amarr Holder. Who does your character dislike more? Discuss.
The Angel. The Amarrian Holder's 'crime' was birth into a society and a position in it (or the ability to gain that position) and the baggage that comes with it. Far as many of my toons go, hating on a Holder for being a holder is quite... hypocritical. Might as well complain that a Federal citizen from wherever was born and raised in his/her/it's environment. Now, various levels of debate exist around what Holder's do, obviously, but that's another topic and even then, that topic is taken into context with the Holder's purpose, stated goals, the fact this is considered normal in Imperial society, and ofc. the cocktail of personal traits and methods for each individual.
The Angel, however, is another story entirely. Your typical Angel, no matter where they are from, have no overlying purpose for their actions that can be considered benign save survival. I, as well as my toons, can understand that. The means employed however are detestable and capsuleers who join the angels have no real need for 'survival' - this is covered by default as part of the whole 'being a capsuleer' thing - ergo all the remaining reasons revolves around personal enrichment. Obviously, all capsuleers aim for this in some form or other, but not all go out of their way to join a faction that see to this need nearly exclusively at the cost of everyone else. Angels, Guristas, Serpentis, Blooders... factions like this offer absolutely no excuse for the capsuleer that joins, and hardly any for your average non-egger members.
The EoM, Sansha and other 'kill all humans' factions is rather self-evident and require no explanation.
In short, the Amarr might get flak for what they do and why, but there are other, infinitely worse offenders out there, and all will be judged by their actions and beliefs, set in context to whom they are and from where, etc.