What's wrong with the fatwa? It's a mild and innocuous fatwa.
The analogy drawn in the article is also invalid because Italy itself, in its entirety, is not holy to any religion. The Arabian Peninsula is includes the two holiest sites of only one religion. Besides, the Grand Mufti or other similarly well informed, educated and knowledgeable people could elaborate on the religious reasons behind such ruling.
In any case, it is not out of hatred for Christians or Christianity but due to the strong Saudi stance against Shirk (loosely translated as "Polytheism", or more accurately, as the "act of associating partners with Allah (SWT), even though such definitions may need further elaboration). As many people may know, most Christians believe in Trinity nowadays, which is considered Shirk by most scholars.