Is there a way to reset the universe so the portal to the ruin is closed and the characters aren't at the outpost?

I believe if you create a new character it will reset.

okay you have to go into your files and copy and past this file some where els (if you want to save your univers) C:\Program Files (x86)\Steam\steamapps\common\Starbound\storage\universe, and then delete it. Then you will have a reset univers.