Here is where both Hitchens and D'Souza get things a bit muddled in my opinion. So here is my take on the matter.
Yes, wars are religious if the head of states are religious.I think especially in years past it is important to realise that the head of sate decided whether a country goes to war or not. Even in the modern day the official decision rests with the head of state, although it is more complicated as the decisions are taken with committees. The point is though that if this head of state is a Christian, then it is against the New Testament for this leader to go to war. So if this leader then makes a choice to go to war it is a religious one as they are denying their belief system.Additionally, for us in the west who like to point out that Islamic countries are terrorist states etc etc. We are saying that these countries are religious when they make decisions to go to war, so how is it any different when a Christian leader sits in the presidential or prime ministerial chair.
On the other hand I don't think one can claim a war started by an atheist leader can be attributed to atheism. I feel I can say this honestly as atheism is not about morality it is simply about the disbelief in a god. So this atheist leader is basing his/her war decisions based on moral principles that come from upbringing and past life experiences and have nothing to do with religion. This is very different to the case of a religious leader whose morals supposedly come from a sacred divinely inspired text.
Here is the full debate. I would recommend it to anyone who has not seen it before as Cristopher Hitchens was a master debater.