@tasby,
Your underlying premise is faulty. Stealing from a religious organization still means that there is a victim; it's the people who paid into the collection plate. They wanted their $$ to be going to alms or even to painting the church ceiling. They didn't intend for it to line some thief's pocket.
1. Of course they should be punished. This is the crime of theft. The law doesn't distinguish between victims' statuses, or even if the victim is human (you can be prosecuted for stealing from the state treasury or a corporation; under your premise, these would be victimless crimes, when they're clearly not).
2. I call nonsense. It doesn't matter that it's a so-called 'higher power'. And that is not punishment enough. We have laws. They apply, no matter who the victim is, or how sorry or guilty the criminal feels (albeit contrition or its lack often is a factor in sentencing. But it is not a factor in a finding of culpability).