I don't think it will throw off white's game much at all. White will put pressure on d5 and b7 as follows:
If there are mistakes or (significant) improvements for either side then point them out and I will try to come up with a new line which refutes 2...Be6.
I had never seen this before, so I checked the Game Explorer to see what information I could find on it. It turns out that there aren't any master games with this position, and it's easy to see why: Black blocks in the e pawn and assigns a bishop to an awkward position for the purpose of defending a single pawn.
Although this move is clearly not the best available for Black, it's still possible that black may try to play it as a surprise to try to throw off White's game. Here are two questions: First, how can White efficiently capitalize on Black's disadvantages listed above? Knowing that your opponent's opening is bad does not necessarily imply that you actually know how to convert it into an advantage. ...Be6 doesn't leave any pieces hanging and doesn't create weaknesses in Black's pawn structure, so there doesn't appear to be a single crushing third move for White. What should White's plan be?
Second, is there any way for Black to achieve good play after these moves? Perhaps the aforementioned problems could be solved by playing ...f6 and ...Bf7, giving Black raking bishops and a respectable pawn center:
Alternatively, perhaps Black might try to exchange off the d pawn to open up the position or fianchetto the dark-squared bishop. Thoughts?