So-- why is the state ordering the church around? If you advocate separation of the 2, then the state has no business telling a church what kind of materials it must use in building o how many exits it must have. Likewise, it cannot tell a church how to dispose of garbage or waste and the police cannot enter church property to arrest a suspect a church may choose to 'harbor,' for the church and the state must be completely separate. I'm sure you really advocate this separation.
Perhaps you mistake local health and safety codes and the "free exercise" of religion.
Local health and safety codes may not impose a barrier upon the gathering, but where and under what shelter may be regulated because the requirement to provide services (medical, fire, police, sanitation, utilities,...) must meet some standard of safety for those providing the service.
Therefore, yes a local community may "tell a church how to dispose of garbage or waste and the police may enter church property to arrest a suspect."
"Safe harbor" is not a guarantee under "free exercise" of the constitution.
It is granted by most authorities out of respect, but just as the Branch Davidian massacre, is not a guaranteed right.
There is no "safe harbor" for fugitives in a church.