Simmons has shown a growing knack for lying. She has completely buffaloed Bobbi a couple of times and Bobbi is like, pro level. Lying is her thang. So Jemma has attained Bobbi level in one season.
Jemma, even more then Mack, is the most wary of powered people, going so far as to suggest putting them down like diseased animals as a mercy. Her attempts to help Skye have included the gauntlets which made her dizzy, but were mainly designed to dampen her powers. She has argued at every turn that powered people are dangerous and should be cured or contained.
The artifact, as we know, frightens the Inhumans. It was designed to destroy them. It has a built in rationale for doing so. It is a weapon to kill them. After being absorbed by the artifact, which I believe targeted her for her sympathies, I suspect she will be transformed into the embodiment of the weapon and while she is not, at her heart, evil, she will be the actual Big Bad of the season.
She will become a killing machine. But she will not be evil. She will just see herself as doing what needs to be done FOR THE GOOD OF EVERYONE, whether they disagree or not. And as we saw with her pretty hard ass attempt on Ward's life, that she is capable and willing to implement her idea of what's right in secret, knowing she would be ordered to, or stopped otherwise.