They won't do us any harm, that would defeat their purpose. Besides if they want to grab you, they most likely won't use the same units that follow you.

[ Ganondorf had not paid attention to the modified people during Jason's event, so at least he had no clue Sephiroth had been amongst them. ]

I agree. I have no doubt they will use what they can to stop us. And we also have to worry about those led by the Princess, even though I suspect their resolve will be broken long before the end of this story, be it by the administrators or by us.