Are you sure about that? He did just reject his gods in the face of despair...
Yes, I'm sure. Moments of doubt do not destroy years of faith, especially not when the doubt is magically induced and subsequently wears off. He may need to atone, depending on his faith and his god, but his religion SAL will remain intact unless he specifically converts to something else.
Side suggestion: what if specific rejection of the Anarch side undid some of the spell's effect - perhaps removing half of the temporary penalty and making the target immune to further reductions for a period of time?)
--No. My original intent was that the spell should punish harder those who more strongly reject the dark side. Specific rejection of the Anarch faith should make the penalties accrue /faster/.
I meant it as a side effect of the suggestion - that once the victim's SAL had been penalized to zero, the caster would be taking a risk in attempting to make a convert: if the victim believed the suggestion, he would either take the offer and be converted or reject it and thereby regain a measure of his original resolve. As a disadvantage for mind-altering "false choice" skill, it would make the conversion part easier to cast, but if it goes against the concept we can easily leave it out.
As far as hitting harder against people who reject Death Metal: we can bonus the spell against Alliance targets in exchange for a penalty against all others, but I'm inclined to keep the spell's effect constant against any given person within that affiliation - that is, a priest with a 2@8 SAL in M1@0 Catholicism would suffer the same penalties at the same rate as a layman with a 1@4 SAL. Consider that the priest is disadvantaged much more greatly by the reduction of his Religion score than the layman; too, I find it difficult to rationalize a preacher succumbing to this effect more rapidly than his lukewarm parishioners.