Just make sure you block low. If you block high, mileena has plenty of time to delay falling into the D1 by choosing when / if to throw the sai.
I agree with the Ermac comments, and also agree that it's not a great idea to throw lightning at her alot. But what I will say is this... Look at the frame data. Under no circumstances does Mileena ever have a true 50/50 that people like to complain about. So, the comment about leaving you guessing because of a counter zoning tool is incorrect.. The closest she comes is with the frame advantage after landed regular telekick without an air sai followup. people always bXtch about that being a guaranteed 50/50, but the fact is... it's not.
In my previous post I mentioned not to throw too many lightning projectiles because it has pretty slow recovery and can easily be telekicked on reaction for +31 on hit. A Mileena player will usually not throw a Sai after knowing a telekick will hit (through counter-zoning) because they will remain airborne and loose their advantage. You should also never stand block the entire EN telekick because as soon as the sai hits (block or hit) she will be at advantage, however, it's not an extremely large advantage and can be countered.
She does not leave you guessing because of her counter-zoning game; you could literally (crouch) block on and off all day from full screen if she doesn't approach you and wait for her to make the critical mistakes. Her guessing games comes into play when you fire off a predictable projectile and get telekicked; at that moment she gets a free jump. She can go low, mid, low+mid, low+low, throw, U+4 which (grants her +9 on block), 2,3,4,Sai block string for meter building or hit confirming 2,3 into roll, etc..... If she successfully gets a combo on you and ends it with a wiffed telekick, the guessing game continues (on both parts).
She has a few options from the free jump in that do lead to a mix-up; would it be considered a "true 50/50 mix-up" that is debatable, but you cannot block her low / mid attacks at the same time (one of which leads to a frame trap). Even though you should crouch block by default and just let go if you see the U4, she still keeps you guessing and that could pose a problem if you're not strong at reads or reactions.
When fighting her as Ermac, I try to keep her withing TKP range and ultimately try to corner her and keep her within the sweet spot. His TKP covers a large surface so I hardly use my projectile (with fear from the telekick) and maintain good spacing. If the match-up is played correctly, she should feel on defense most of the time and will start to take risks; at that point you can capitalize on her mistakes lather, rinse and repeat.