Backup your stuff in the unlikely case you have a problem.
Take everything off your ship. You could use a scanner and move it all at once to a planet LOL. Short of doing that, any persistent container mod would be helpful because you can move entire containers at once with your stuff still inside.
Either way take everything off the ship you intend to keep.
Stuff that this mod adds you won't be keeping either way. They'll be "perfectly generic items" when you're done.

This is important because you're gonna loose that tech too. If you forget, you'll need a program like Starcheat to fix your character.

Go to /starbound/storage/player/ and delete your .shipworld file
Open Starbound and load your character. They'll have a new ship upgraded fully to the last tier you unlocked. Without any other shipmods, you'll have a vanilla ship. With a different shipmod, you'll have that ship.