This simply means that Congress (the only lawmaking body) cannot make any Christian sect or any religion a state religion. This does not mean that the government has to exclude all religious prayers or activities from government. It also means that Congress cannot keep any Christians from practicing their religious beliefs or modify that practice according to their liking.
Since Congress cannot make a law to make a state religion or abridge religious practice, there can be no law that does so. Therefore, if anyone wants to pray for the police or any other government officials he can do so, and if any government official wants anyone to pray for him, he can request people to do so -- there is no law that prohibits it.
The opinion of atheists is that there is no God, so prayer is of no effect. But if it has no impact in their minds, then what's the issue? Besides, there are many who have prayed and received answers to their prayers and, therefore, do believe that prayer works. Why should government bend to the opinion of these negative naysayers who have only opinion to go on? Our country was founded by those who believed in God for believers to practice their religion freely, unlike the oppressive country they left.
Whether prayer actually works or not, it's clear as day that since Bible reading and prayer were banned from schools, test scores have gone down (until the tests were dumbed-down, anyway), immoral behavior has increased, violence has increased, drug use has increased, and our society in general has declined.
Atheists don’t think there is any benefit from praying but there is an obvious negative effect since we publicly banned God from the public square. Should we conclude, then, that atheists want more destructive and negative effects for our society? It certainly seems that way since a prayer can do no harm, whereas turning away from God appears to be having terrible effects on our world.