Well, to be fair, SeeD was created in order to protect the world from Sorceresses. But even so, they wouldn't come for Rinoa unless she went evil. And if they did, Squall would stand against them. If Rinoa weren't being mind-whammied by Ultimecia, she'd know that.

"I'm your Knight!" he insisted. "I swore an oath to protect you! I'm on your side no matter what!"