Don't forget that everytime Mileena rolls Reptile, she can combo it with a JK or JP/air sai. I would say this is the most unbalanced match in MK2, as everyone probably knows. I do think it is a lot of fun however, because it is so challenging. And it IS winnable with Reptile...
REPTILE
His invisiblity is definitely the key. Pretty much any Mileena short of the best ones, will see him go invisible, panic, and either roll or drop kick. Expect that immediately after you turn invisible, block her attack, and punish. Also, you absolutely need instant acid spit with analog, so that when she spams, you can time your acid without trading hits with her sai. Slide is awesome when Mileena tries to charge in on you. Mileena isn't threatened in this match, so she probably won't block a lot. Roundhouse to keep her away (though very tricky when she mixes it up with air sai), and to remain invisible.
MILEENA
Mileena can do just about anything she wants here and win. Sai are her best bet, but won't earn you any respect points if you just spam them to win. I prefer to jab so that Reptile can't really do anything. Also, I love throwing ground sai, and baiting a JK from Reptile. on MKAK especially I can often do an aaHP/roll/JP/air sai combo off of his jumping at me.
For me personally, there are harder matches in MK2 to win than beating Mileena with Reptile (beating Jax with Reptile, i.e.).
All in all, a 9-1 matchup in Mileena's favor.