Pumpkid
~Vibing along the cosmos~
lol She's joining because Zekrom is captured and she's the only one that he trusts so they make use of Zephyr while she stays there learning the map and trying to figure out how to set him free. Maybe she can have at least one of the team members like Ray and inform him the truth of what her plan is. Being a lab assistant can come in handy to break them loose. She would probably occasionally fight yall to prove her "loyalty" but wouldn't dare want to really hurt anybody.There's also option 3. Out of sheer pity Zephyr orders her duskull to turn invisible and take out the group for Violet which in turn leads her into believing that she did that on her own. Nah I'm just messing around I would be perfectly fine with any of those scenarios.
If anything where to cause Zephyr to fight against Team Plasma it would be Ghetsis. Perhaps Nero and Reshiram are on the verge of being defeated by Zephyr and Zekrom with Ghetsis openly gloating his victory to the group and accidentally spills the beans that the only reason he allowed Zephyr to join Team Plasma was because she had some control over Zekrom and she was the perfect tool for helping him conquer Unova.
Edit: just read your post stitches and I love how Violet's confidence flew out the window the minute Zephyr's duskull appeared
But yee she doesn't approve of their ideals