Sorry but our Military isn't a puppet like our government, no matter how many top level officials are replaced in favour of pro-Indian ones, we will always have lower ranking officers who outnumber higher level one greatly (common practice) and soldiers are always anti-Indian. It's not a fraction, it's quite a large amount, the little fraction are pro-Indian.
No, we will probably not be using it against India but the Indian Army will be quite foolish to not take a possible war into account. And I am quite sure they did.
Also, the reverse engineering is an issue. China hasn't been offered the Brahmos and will probably not be due to Indian involvement in it (India wouldn't want it). A duel project conducted by Bangladesh and China for a new anti-ship cruise missile derived from Brahmos will definitely interest Bangladesh Military, especially if the only thing they need to do is secretly deliver a few of those missiles.