It wouldn't interfere significantly on the military prep, but it would on the Politicians.
If/when the church was to throw in their two cents, any politician who wanted to stay in government would have to listen and act accordingly. The religious vote is powerful - take the US bible belt for example. What percentage of the population there is going to be listening to the Pope and other religious figures in preference to the politicians and Generals.
Once the ball was rolling though I doubt the church would have a lot of influence, but they'd be major factors in the time leading up to the decision to deploy. They might even have influence over the timeframes and manpower involved in the deployment.
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If it moves, shoot it, if not push it, if it still doesn't move, use explosives.
Nothing happens in isolation - it's called "the butterfly effect"
Mors ante pudorem
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