MK9 was a series reboot in terms of gameplay, not story. It begins right where Armageddon left off and the whole story is based around Raiden changing the old timeline. If it was a complete story reboot, there would be no old timeline.
They can indefinitely delay it by preventing Onaga's return. I think we're gonna see that happen in either the comics or the game's story. Raiden might kill Shujinko and hide the Kamidogu away, or defeat Blaze and the dragon priests guarding Onaga's egg in order to deal with the egg somehow.
Shinnok's invasion is still gonna happen, but hopefully we don't see a repeat of the Deadly Alliance and Onaga storylines. They need to stay in the (alternate) past.