Think of Siege of Lothal as a 2-part special, inbetween both seasons. Similar to how Doctor Who does it's Christmas Specials.
And I fear Disney won't EVER do Thrawn. He is too beloved, and there would be so much backlash from ever critic saying "Thrawn would NEVER have done THAT", or "Thrawn would have seen through that ruse easily".... he is on a pedastal so high than few could dare portray him to the satisfaction of the masses.
I think Disney will do Thrawn. And I think that when they do him, he will be better than he ever was before.
Ideally, that means current Zahn doesn't write him.