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The Jews were military allies of the Muslims in some areas. It was apparently the case in Jerusalem. I read about this awhile ago and can't find that source. It takes some work to dig up a real history of this area.

Anyway, the Christian population of Jerusalem had been expelled into a devastated land to starve prior to the arrival of the Crusaders. The Crusaders came upon the survivors of this action and it was a reason they used to put to death the defenders of the city after it was captured.

Here is a source that references that action,
"Within the city a large Fatimid Egyptian force was awaiting their approach. The Egyptian army was well trained and had carefully stocked the city with arms and provisions in anticipation of a protracted siege. Jerusalem's most topographically vulnerable northern fortifications were strengthened. In the surrounding countryside the defending Moslem army had poisoned cisterns and conducted a scorched earth policy in order to deny the advancing Crusaders vital supplies. In order to avoid possible betrayal from within The city's Fatimid rulers expelled its Christian population prior to the Crusaders'arrival."
http://www.biu.ac.il/js/rennert/history_9.html

Here's a book I think would be very instructive (I haven't read it) "The Jew As Ally of the Muslim: Medieval Roots of Anti-Semitism"
by Allan Harris Cutler and Helen Elmquist Cutler
Commentary, http://www.danielpipes.org/article/33

"The Jews were military allies of the Muslims in some areas"

I really doubt this. The 'Israelites', as they were called, did not constitute a compact political entity in any part of the muslim world of the 11th century. But killing the whole population of a city after its defeat was very common. As there was no way to identify friend from foe, especially when they both spoke a same completely different unknown language.

But the fact that Jews were then living in 'relative' peace within moslem communities in the moslem world is very well known to the scholars. Look at

http://en.wikipedia.org/wiki/Maimonides

You might as well have a small idea of what was the intellectual mood in the 12th century.