I think you are forgetting something important. When someone casts a spell, you do NOT know what that spell is about to do. If you use your skill rolls you might be able to identify the spell being cast and be sure it is safe to accept.

This has a major implication. The harmless descriptor is not something a character has any idea of unless they can identify the spell being cast with a skill check. I could say I am healing you, roll a bluff check, and cast Harm instead. Unless you identify my spell, you are left with the option of trusting my word and accepting the spell or trying to make a saving throw.

This applies to the debate here for the following reason: You do not know what a spell does unless you succeed on a skill check. Therefore you do not know a spell is harmless unless you succeed on a skill check. Therefore a harmless spell cannot automatically bypass natural defenses Unless you suppress them because your natural defenses have NO way of knowing the spell is harmless.

Ruling otherwise is a perfectly acceptable house rule. I've played both ways and both are fun and interesting. With regard to rule intent though, I think it is clear that SR is supposed to apply and my argument is the reason why.