The difference is Gemma is a professional nerd and has always been. She has 2 PHD's, a biochemist and she didn't join SHIELD for spy shit or nation stuff, it was the best way to find answers to her science questions. She and Fitz are seemingly the best emerging scientists in SHIELD and they seem to be the best surviving scientists, she's all about the science, her loins would melt at solving a math equation.
She is written as one of those cute little meek scientists, that couldn't hurt a fly, and when push comes to shove and they have to shoot "the big bad" to save their friend, they can't and their friend dies, and they have to live with it for the duration of the series, and when they find the big bad at the end, they have an epiphany, throw down their gun and say, "no, i don't have to kill you", then big explosion and the big bad dies from an external cause, the way her character is, she would throw down the gun and say "i'm better than this" or some bullshit.
nope, not ONLY did she plan to murder ward, she chose a weapon she could use, cuz she's probably really suck ass with guns, so you know, something up close and personal that will kill in 1 second and be an assured death. She knew how inept she was (cuz she is a scientist, lets be real) and compensated with the diviner disc.
All these other characters, suck ass emo syler, "wah i love watches"
or Ben Linus "wah, my daddy didn't love me"
could be evil, are evil, we knew they'd be evil, plus they're not nerds, just socially inept.
Gemma is a super nerd of the highest double PHD, and she wanted Ward dead, hell, she even saw how they dismantled Deathlok, and she was heartbroken and sad, but still said.
"hang on, i've got some murdering to do first"