I never heard it was disowned but it did cause John Tobias to leave Midway due to creative differences.

Theres nothing really in the game that couldn't be added into the main series however.

But then again they just had a chance to include a couple of Special Forces characters and they havent. Not even in the bios.

It's not canon.

MKSF took place before MK1 and had Jax traveling to Outworld at the end to stop Kano from stealing a magic gem that opens portals but all indications are that it's still canon Jax had never heard of Outworld before MK2.

Also, characters like Gemini, Tremor, and No-Face have never even had their names mentioned ONCE in a single canon game, implying that they simply don't exist. If they did exist, they would've at least been name dropped during a Konquest or in a Krypt item.