The answer to this is twofold. Firstly, explicitly atheistic regimes have perpetrated more than their fair share of atrocities.
Secondly, lumping the diverse realm of transcendent belief systems together as a single phenomenon “religion” is willfully simplistic. For example, a religion inspired by a political and military leader is likely to differ in complexion from one whose followers attempt to emulate one who lacked all worldly power and preached a kingdom “not of this world”.
I do not wish to defend the crusades, but the grievances harboured by Muslims are unjustified. Early Islamic conquests were simply imperialistic expansion, and Christendom’s campaigns to reverse some of it may have been similarly ambitious, but were a response to prior Islamic invasions. Mr Allan should be careful to avoid the charge of hatemongering: stirring prejudice against a group because they share an irrelevant characteristic with some miscreants.