Well I can understand how people would react if they saw the church they attend be desimated and consider it bad taste the same as those who think that Mass Effect is bad because of the sex scene. (Boooooo Utah...) but at the same time, even if this is sarcastic or not, would the aliens care where they attack....? I've not played resistance but it seems like from the alien mindset that if people run into a building they think that can protect them, wouldn't it be a prime target? similar to army bases or subways, etc.
It mnight have been sarcasm, unless they just had a church in the main cities, that you could go in if you wanted, but its just kinda there.
