We have quite a few proven ways to violently turn the whole of society against some group:
- make religious people appear as haters of humanity, who even if looking normal, could turn horribly violent without warning; and are therefore to be feared unconditionally.
Example: we already have that when just speaking Arabic can get other passengers to call airport security. Extend that from Islam to all religions. After all, you can find acts of violence committed in the name of each.
- equate religion with drugs: believers are "hooked" on the surreptitious gratification of their "delirious rituals". Make it just another probable attribute of the thug who scares you in a dark alley. After all, if they are persecuted, religious people probably are rejects of society; and many of them will actually end up in the street unwashed and in desperate need of your wallet...
- accuse them of conspiring against the social order. Once religious people are forced to hide... who knows who might be secretly religious? Any national problem, from tragedies to annoyances, can be claimed to be caused by a secret cabal of religious people, who congregate in secret to act viciously and hatefully because that's how religion makes you (again, no lack of examples for your propaganda).
Once you do all this (don't worry if the accusations are inconsistent, people won't notice) ...you won't even need police investigations, or rewards for snitches (although do use those, for good measure). Anyone having the slightest suspicion will report it to the police simply because he believes he is protecting himself, his family and his community from a terrible evil.
Even religious people themselves, if they are efficiently cut off from their religious community by this continuous surveillance, and their lives are made suitably impossible by the continuous paranoia of being informed on by even the closest human connections, will eventually start doubting that the propaganda is right, and they have been part of an inhumane delusion all along; and finally almost certainly either go mad, commit suicide, resolve to "go straight", or even denounce themselves to the authorities.
In which latter case, of course, you should send them to a harsh camp for a few years to "reform" them; then if they seem repentant enough, fully pardon them and parade them as public example that no religious delusion is hopeless, and that it is possible to recover sanity and become a "good citizen" again.