Does playing the King's Indian against the Benko put black at a foreseeable disadvantage? I am currently in a turn based game where white opened with 1.g3. I clearly see that white probably (at least white should) will fiancetto his king's bishop on the next move, aiming to control the white squares. 

I google'd 1.g3 and saw it's called Benko's Opening, and as I suspected will likely transpose into something else.

It's tough for black to know exactly how white will attack, and the king's indian does fit that scenario (not overly aggressive, gives options, and also doesn't give white a full center advantage). 

So my question is, giving a game that started with Benko's Opening and black plays King's Indian, does this put black at a foreseeable disadvantage where white would easily be able to capitalize?

I can see the opening possibly taking this route

[FEN ""]
1.g3 Nf6 2.Bg2 g6 3.d4 Bg7
No, there is nothing wrong with this approach for Black. A kingside fianchetto is a perfectly reasonable response to White's. You are likely to end up transposing to an actual King's Indian if White eventually plays c4, in which White's fianchetto is a fine setup but not a killer.