What’s hard is affirming the child’s ability to think for themselves, while still maintaining your expectation that they do what they’re told. I suspect the answer has to do with picking your battles well.
Generally speaking, it has to do with thinking out their boundaries and teaching them to put boundaries on themselves that they ought to put on themselves as they get older. Don’t make the boundaries more restrictive than they really have to be, but rather the kind of boundaries your children will choose for themselves. You can even say, “I’d put this boundary on myself, and this is why, whereas I’m going to insist on at least this boundary for you, and this is why.”
For instance, if you hate the smell of some kind of gum, ask yourself whether the boundary you put on that gum is only the same boundary you’d put onto yourself if the tables were turned, which in turn ought to be the kind of boundaries any polite person would have. If your child had the same reaction to your gum as you do to hers, would you quit buying that gum? Would you buy it, knowing there are plenty of times to enjoy it without her around? Would you tell her to suck it up, it isn’t that bad? Teach her to do the minimum you’d expect yourself to do, and meanwhile do the maximum that you teach her to consider doing.
The last thing, however, is very important, and even a part of catechism classes intended to safeguard children from predators. That is teaching your child which boundaries are hers to decide and how to oppose those who would try to violate those boundaries by the various means that predators use: intimidation, guilt, manipulation, extortion, and so on. Insisting that she not have to hug or share any other physical intimacy with anyone she does not want to is an example. She has to say, “hello” to the relative who gives her the creeps, but she does NOT have to let him hug her.