When Markus first learned of the Mutant Decree, we decided he should doubt himself rather than let it gnaw at his Faith or his belief in the Law. That rules Conviction right out, since Markus does not have the self-esteem he needs for that.
[X] Faith
I don't think Markus' Faith is wavering. When he faced the daemon in the sewers who taunted him of his past, Markus stood his ground and banished it. He obeyed High Priest Ethel despite his misgivings due to Ethel's position in the church, only to turn on him after he saw enough proof to know that Ethel was not doing his job properly.
Markus' Faith is still alive and well.