It has always been a difficult situation. A country’s leader has the responsibility to defend his people, and the Church has always taught that there are just wars. And individuals can certainly defend themselves and others.
However, the interesting thing in the situation with Peter is that Jesus was not telling Peter that he could not defend himself with the sword, but that he should not defend Jesus with the sword. In other words, for us, the “jihad” is forbidden. The blood of martyrs is the seed of the Church, and I think that is how we have to look at it.
The Christians of Iraq should not take up arms against the Muslims. However, beyond that, it’s ambiguous.
The early Church forbade Christians to seek martyrdom; they were supposed to avoid it if possible, but not to renounce Christ if martyrdom came to them. But this was also accompanied by preaching and by support from other Christians, and I think the thing that is lacking to the Christians of Iraq is (a) any serious effort outside of Iraq to convert Muslims and (b) support from Christians outside of Iraq.