Well of course you can make it not affect alignment.
From \Fall Further\Assets\XML\Gameinfo\CIV4ReligionInfo.xml
The interesting part (concerning alignment) is in the end.
<iAlignmentModifier>-175</iAlignmentModifier>
Change the value to 0 and it will not move your alignment either way. When using broader alignments.
If you prefer the more rigid aligment system, these lines are what you are looking for.
<Alignment>ALIGNMENT_EVIL</Alignment>
<AlignmentBest>ALIGNMENT_NEUTRAL</AlignmentBest>
<AlignmentWorst>ALIGNMENT_EVIL</AlignmentWorst>
If for some reason want to play a nation of good backstabbers (yes, I see the ambiquity). Change them to the following. They are the same as for Fellowship of the Leaves.
<Alignment>ALIGNMENT_NEUTRAL</Alignment>
<AlignmentBest>ALIGNMENT_GOOD</AlignmentBest>
<AlignmentWorst>ALIGNMENT_EVIL</AlignmentWorst>
Alternatively, if you wanted them to always be neutral, this should do the trick.
<Alignment>ALIGNMENT_NEUTRAL</Alignment>
<AlignmentBest>ALIGNMENT_NEUTRAL</AlignmentBest>
<AlignmentWorst>ALIGNMENT_NEUTRAL</AlignmentWorst>
I hope this helps.