If she does a regular telekick, you don't have to block low with Smoke. Punish it (and the roll) with 3 2, 3 D1 2, 2 1 Smoke Bomb, and any ender of your choice (F4, Jpk+grab, etc).
For the EX version, you can block the first kick high, and then immediately block low before the second one lands. Now, either uppercut, or use D1, D1~Smoke Bomb (almost impossible to do online), and combo her.
You can jpk+grab her when she uses D4, or, even better, counter it with a faster low poke (D1/D3). If you're familiar with Smoke's poke game, she may be trapped. Hell, if you're ballsy, you can throw a blank Smoke Bomb if she tries to D4 her way in.
As of now, this matchup is definitely in Smoke's favor, but Mileena can always be tricky and tough, regardless.