As a lawyer, years ago I attempted to legally define religion. To my surprise I learned that because of the Separation clause of the First Amendment, courts in the United States have refused to legally define religion. Therefore there is no legal definition of religion.
Thus the separation clause which states that " Congress shall make no law respecting an establishment of religion" is itself under constitutional law too vague to be enforceable.
Subsequently, Federal and state courts adopted the separation clause as a restriction upon their review of issues which may be tainted with claims of "Religion". As a result, injuries have been judicially allowed to be inflicted upon citizens of the United States with no recourse or recompense at law or in equity.
The only way to define religion is by the elimination of certain activities generally considered to be non-religious in nature. In that regard, activities of business, crime or politics reduces a claim of "religion" or "religious" activity to such things as worship (with no definition), prayer (beseeching an indefinable Deity), Mass ("religious" gathering), doing good works, living a "religious" life, administering "religious" thought practice and its exercise.
Any activities clearly outside the scope of those indefinable activities are clearly not protected by the separation clause imposed upon the congress by the constitution or unjustly adopted as a restriction upon the courts.
For example, murder of a member of any religious organization is not protected nor is the orchestrated murder of any non member of any church for purposes of protecting the security or image of that church.
When such activities are discovered it becomes incumbent upon States, federal authorities and courts to separate the non religious activity from the protected "religious" activity.
In doing this, appropriate state and federal prosecutorial officers are required to make a conscious separation of activities of any given church into at least two activities which would be "religious" and racketeering.
Thus, the church, its officers, and any participating members in any definable racketeering become liable and vulnerable to criminal prosecution.
As an example, if the Pope ordered the death of any individual, he would be transformed into a "religious" criminal. The same goes for the head(s) of any religious organization otherwise protected by the separation clause.
Most crimes have a statutory limit on prosecution for a certain period based upon the crime committed.
In the case of murder or conspiracy to commit murder, there is no statutory time limit between the murder and/or conspiracy and time of prosecution. Murder is a heinous crime outlawed by most civilized governments, therefore whenever it is discovered, prosecution is ripe no matter how cold or stale is the discovering of the crime.
As to the issue of a church being prosecuted for criminal conspiracy to commit murder or any other crime a prosecutor would likely be branded as a persecutor not a prosecutor.
Of course as all any attorneys will agree, not all crimes are prosecuted. It has become the privilege of prosecutors to have a discretionary right of determining whether to prosecute or not.