Well, as there is a Talon of mine sitting on the Rager's pillar it is possible to be a non-mainstream follower of Shokai. However, it's probably one of the harder tasks to tackle in CF. Since the moment you've killed a good, regardless of what your character percieves it as, you have committed an act that goes against the very base of Shokai's religion. Over the years people have asked 'what if I play a character who does evil, but doesn't see himself as evil, what alignment should I pick?'....the answer is always 'evil'. This applies here because you're asking if Shokai looks only at intent or if he looks at actual actions. Both, is technically the answer, but raw actions will almost always speak louder than intent. So if you're out hacking up goods by the dozen because your character believes they're all tainted and corrupting themself with magic, the fact doesn't change that you're out killing goods. To toss in a movie example, if you remember the last few scenes of A Few Good Men after the judgement is handed down and Private Downey looks incredulous and asks 'why', and is answered by Dawson with this long schpiel about 'it doesn't matter that we were ordered, we still did a bad thing yada yada yada'...it applies here too. Maybe magic really is the root of all evil, but there's probably another way to get rid of it (as a Shokite) that slaughtering everyone who uses it.

So, the answer is yes, you can be a non-mainstream maran. However, it's not easy and you should probably look into alternate ways of accomplishing your goals where goods are concerned.

My perception is that as a follower of a religion, regardless of personal views, is that you follow the religion. Though there may be instances where you do not understand or are tempted to do otherwise, you still must be devout to the religion. I would think that religion is not something that is easy to follow, and sometimes will lead to conflicts with one's own way of thinking. Though this example has been a bit of controversy lately, I would point to how most Catholic priests take a vow to abstain from sex. It dosen't mean the desire isn't there, instead it is what they must do. Just my thoughts.