You're correct about the teleport being an anti-zoning tool, but I should tell you that Kitana's ground fan recovers fairly quickly. I have been punished for trying to react to this with teleport at times, so I'm forced to be pre-emptive unless the Kitana player is predictable. Now against an air fan, it will always be punished by teleport due to the added landing recovery from throwing a fan in the air.
Personally, I don't want to take to the air against you due to the threat of a full combo from an air fan unless you throw one when I haven't pressed a button yet. As well, your EX Rising Fan does wonders as an anti-air.
For the air-to-airs, isn't Kitana's jump-2 five frames or am I remembering wrong? Because if it is, it's one frame faster than Scorpion's jump-3 so it ought to be winning the exchange. If not, that could be due to hitboxes and active frames favoring Scorpion. However, remember that you have the float. I feel it does wonders with faking jump-ins and improving your air game.
Another note to take: if you can't beat Scorpion air-to-air, then the next time he jumps at you when you don't have meter, run under him and mash your fastest possible combo string. If he does a jump-3, it will whiff as you run under him, and he will suffer landing recovery which gives you the chance to get a combo.
As for Ninjutsu's 50/50s, I know this may seem hard to do, but the sound of a sword being drawn is the audio cue for Scorpion's F2. The first hit is still mid, so you can block that crouching, but the second must be blocked while standing. If they cancel into a Takedown instead of going for the overhead, it will always hit at a later frame than the overhead. I recommend practicing a fuzzy guard against this. It's much easier said than done, but it's certainly possible.
Now, it will be unrealistic to expect that you can fuzzy this 100% of the time, so don't stress this if it still hits you at times. I have taken to adding in ways to catching the opponent by surprise with F2 and I don't even need to use F2 - Takedown to coax them into blocking low. For examples of this, see my YouTube by clicking my signature.