To think that back in the day, they wanted Fabula Nova Crystallis to be twice the size and scope of the FFVII Compilation, with at least six (self-contained) entries, including perhaps a full feature film and some other media like books. I won't even be surprised if they had planned an anime series as well. =P
"Haeresis" would have seemed a little redundant for me. We've already defied an established global religion in FFX. We've been beating up sci-fi Pope a few times in FFXIII. We've slain god after god in the JRPG genre. LR's sinister cult and its intense hatred of a "wicked Saviour" (thereby being heretics to Etro...I think) perhaps could have been pulled from whatever basic idea or premise someone had in mind when they first trademarked the name in 2006.
Actually come to think of it, what about an RPG equivalent of the Spanish Inquisition? You're not the heretic. You're the trusty acolyte-turned-warrior possibly wielding a Templar cross on your chestplate and shield, tasked with flushing out heretics and to punish them whatever way you can. No one expects the Spanish Inquisition.