SpiralKnights is a java applet. As such, it can run on any system that supports java (mainly Linux, Windows and Mac, although there are others).
Steam also supports the Operating Systems of Linux (officially the Ubuntu distribution), Windows, and Mac.
However, despite the OS support overlap, OOO does not support the use of SpiralKnights on Linux, through Steam. For someone that has bound thier SK account to Steam, and then forced to use a Linux operating system, this poses a problem logging into the game.
I've tried to run Steam through WINE, and launch SpiralKnights from there, but it crashes upon some basic command key use.
Is there a reason that OOO has not allowed the use of SK through Steam on Linux?
Or is there a way to unbind an account from Steam?
Just so I don't get anything confused right now, I'm stating that I think you said this: The pure Spiral Knights software runs fine on Linux. The Steam version of Spiral Knights doesn't run on Linux. You're wondering why OOO doesn't support Linux.
The answer is that OOO is currently down one programmer right now and is having a harder time cranking out content. I can't blame them for not supporting an OS that is very uncommon.
If you want to get your account switched off of Steam and onto OOO's servers again you're going to have to contact support about this as they have stated in the past that running SK on Steam instead of the base client is a one-way affair.