[Fyron]

is there any way to force the alien player to strip the ship of components and replace it with hive sections at a space yard before they can use it?

Sure. Give 1 boarding defense ability to every component that you want to be destroyed upon boarding. As long as the tech needed for them is unavailable to the Aliens, they won't be able to repair such components and will need to retrofit the ship. You won't be able to use the "Only Security Stations" damage type very well, but it might be ok. Also, this does increase the boarding defense of ships, so you might want to increase the boarding attack values of all boarding party components by an appropriate amount to compensate.