I'm building a remote setup with my Raspberry Pi, and I really love Ekos as a tool for automating my setup, but I was wondering if it was available as a standalone program, apart from Kstars.
If not, is there any similar program available on Ubuntu/Raspbian for the Raspberry Pi?
Nope sorry it is only available within KStars. If you want something else perhaps you can use the scripting tools to build something custom to your setup.