As I understand it, red is a sign of corruption in the cosmere. I just reread The Emperor's Soul, and it mentioned wisps of red smoke when Shai tests the Soulstamps. Does this mean she is corrupting Gaotona's soul?
Yes, that is what that means. Corruption doesn't have to have the negative connotation, right? Basically, it means an outside influence is changing the Spiritual nature of the soul. And, yeah, that's exactly what is happening right there. Now, I would call that a pretty good thing, but... like, all of those things, where she is playing with someone's soul, and changing it, and changing their past, and things like this. This is, by cosmere definition, corrupting someone's soul. That's expressly what it is.