Rubia no longer compatible w/ Krastorio 2 Spaced Out, I had this enabled due to the K2SO description now I am not sure how to go about loading my game without Rubia. Any suggestions on if I could remove Rubia dependency or anything else?

Assuming your save file already had Rubia and Kras2 Spaced Out enabled (and far enough in that you don't want to restart) you can start by disabling Rubia, Rubia Assets, and Rocket Cargo Insertion (its two dependencies), then disabling this mod and attempting to load your save file (ignoring the little warning that tells you about missing mods)

If it runs and doesn't crash, then you're golden; save your game under a different name (just in case there are long-term issues, keep the old save).

How can you disable Rubia, and it's dependencies, when this mod, Enable Planet Mods Lite, is marked as requiring Rubia?

Rubia needs to be marked as optional until sometime in the future where it is compatible with K2SO.

The only option I know of is to redownload the old Rubia version and just don't go to Rubia until it gets updated to be compatible so I can continue using this mod.

Please re-read the previous instruction, specifically the part that comes after disabling Rubia and its dependencies:

then disabling this mod and attempting to load your save file

After you re-save your file, you won't need to manually enable or disable any mods. The save itself will sync up the new modlist, without Rubia, its dependencies, or this mod.

For a more long term alternative solution, unzip this mod, rename the mod folder and the mod name inside its info.json, then remove Rubia from the info.json; that way, Factorio will consider it a separate mod from this one, and won't attempt to auto-update it. You can use that instead.

As for your suggestion about marking it optional within the main mod; maintaining compatibility with Krastorio 2 Spaced Out has never been on my list of priorities for this mod, nor has it ever been suggested as a recommended mod to use alongside this modpack.

Any issues between K2SO and the planets that are part of this modpack should be taken to the developers of K2SO and those planets instead, as they are the only ones who can resolve the issue. Besides, according to this thread on the Rubia discussion page, K2SO compatibility is currently in the works. I'm sure they'll work it out soon, and until they do, you have both of those temporary fixes available to you.