From my understanding a torah scroll written by a heretic has no sanctity and should be burned (Gittin 45b). May one read torah related material, written by a heretic but that contains nothing heretical, in the bathroom? Similarly may one read the koran in the bathroom since the Koran contains references to Allah which is ostensibly the same thing as Hashem (as opposed to "in God we trust" on currency which is a generic term)?
A Torah scroll which is written by a heretic should be burned ,like you said. However, if one did not burn it and brought it into the bathroom that's also fine,but once one starts thinking about Torah in the bathroom that becomes a forbidden act (Shulchan Aruch OC 85:2). A Torah written by a heretic is not holy but if it is exactly the same as a kosher version then learning from it will bring thoughts of divrei Torah.
Rabbi Nachman from Bratslav teaches that a person should always minimize his or her time spent in the "throne room" because of the spiritual impurities present in filthy places. Likewise, Rabbi Mordechai Machlis once told us that Rabbi Avigdor Miller (a teacher of his) would keep in his bathroom a copy of the New Testament (i.e. Christian scripture) and Quran. Ostensibly, even if he would read them, he would probably take care of his "business" as quickly as possible in order for him to get out of the place of spiritual deficiencies. It perhaps may be permissible because they do indeed contain heresy, which is spiritually impure, which is allowed in the bathroom. Not that it is necessarily required to read them in the bathroom. Tzarich iyun.