From the link, it is not the Pope who’s views are reputedly reflected in this, it is reputedly “a group of Jesuits in Rome, is a very special magazine. Every one of its articles is reviewed by the Vatican secretary of state before publication. So the magazine reflects his thought faithfully.” That’s a bold assumption to make. There are few editors who personally approve and believe 100% in everything they review for a publication. To me, this article represents an op-Ed piece, but then that’s my non-Vatican scholar view.
The Vatican is not “condemning Islam” (although Catholic-haters would certainly like to put that spin onto it). The Vatican is condeming religious persecution. From the same article:
Also, the Vatican understands what most people do not- that a holy war doesn’t necessarily mean a war.
More so than actual war, jihad refers to the war between good and evil in onesself. Followers of Mohammed should always be fighting to purify themselves of the evil within. The holy war concept is secondary; the Vatican realizes that Muslim states are not about to invade Western Europe. As far as the rest, Dogface did very nicely in summing up the actual point of the article.