On the memory modification of the agents. The modification is legal since it's consentual (though without consent the Husk cannot be used).
On the issue I think you're getting at. It's almost like Sprites, except the Husk really is just an empty body. For instance, when a character dies, an empty body is created and an old backup applied. This is just like that, except the empty body is created for use during a mission. Then when the mission is done, the cover can be kept by just transferring different agents into the body, while still allowing them to come and go as necessary. The memories that are extracted from the agents are so that there is no need to completely relearn everything for agents.
This however doesn't change this one simple fact. The body cannot move or think or anything. It really is empty, until you insert an agent. Which is why it bypasses Yamataian law concerning this. Sprites could move, they could think, heck some even had personalities. Not so here. This literally is exactly like a backup body. If this were in violation of the law, restoring an ST backup of a person would be as well.