The point being : one is not allowed to hold funds in online wallet accounts unless it is permitted by the RBI. When you talk about any "company" being able to wire transfer into India , yes it sure can. But do you think BTC-e will be liable for any wrong doing ? Of course not it will all come down on the individual doing the wire transfer in the first place. There is a reason RBI does not allow people to hold online wallets in services like paxum and payoneer. I'm sure the same principles apply to a btc-e account too, since it is an online account held under your name/pseudonym without any AML/KYC procedures being followed.
That you can prove that these funds are/were legitimate is another story in itself. Of course I do not agree with the RBI guidelines, since its just under the pretext of them not being able to follow the money trail. They should allow such accounts to be held. But then again that's another story in itself.
Again I am open to being corrected. Sorry if this is getting too long.