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I do not know for sure, but I get the feeling that though the Heretic's were introduced in 2, they had not been buying what the Prophet's were selling for a reasonably long time. In H2 the Arbiter is tasked with wiping out the leader of a rebellion, and it takes a while for those to gain enough steam to be a threat to an established hierarchy, so they were around during Reach, just not as informed about the real story of the rings by Spark at that point.
[Edited on 08.10.2010 10:07 AM PDT]