Baldur's Gate : The Sword Coast Chronicles : NWN2 Persistent World

So in order to get the Spider Domain you'd have to be a cleric in service of Lloth or Seveltarm according to the wiki.

This would mean you're a worshiper of a dogma that as part of its tenants has the rule to not harm spiders, right? (Yes other drow may not care about harming spiders, but that is irrelevant since they would not have the Spider Domain and hence not be in direct service to this dogma.)

Why then is the Spider Domain's perk the ability to turn spiders, an action that harms them in-game?

Evil clerics rebuke undead (or in this case, spiders) which is not the same as a good cleric turning them. It is not a physically harmful action (rebuked creatures cower in awe of the cleric's evil channelling of the negative energy plane rather than in holy terror of the positive energy plane that good clerics use).

BGTSCC has not yet incorporated Command (dominate) for evil clerics instead of Destroy but it could be something worth considering (Sigil has it, for example).