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The question remains unanswered, was Earle Cooley a scientolotist?
Nope he was not. The joint is run by lawyers and yet present time still in members Scientologists believe the joint is being run by the great thetan DM.
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Having observed Earle Cooley, up close and first hand, IRL, it was obvious that Cooley feared Miscavige. Miscavige was definitely his boss.
As for becoming cozy with the the U.S. government, Hubbard repeatedly tried to do that, not only with the FBI but with the Defense Department. Remember his famous letter to JFK, circa 1961?
In 1969 Hubbard had no problem with the idea Scientology receiving government funding.
Does anyone seriously think that Hubbard didn't, ultimately, want a "deal" (or "arrangement") with the IRS?
It's more likely that there's a condition of mutual blackmail & mutual benefit underlying the truce between Scientology and the IRS.
Scientology helps the IRS by forwarding (tax and income related) information obtained during (Sec Check, withhold pulling) counseling sessions (in the event that members become "anti-Scientology"), and the IRS helps Scientology by leaving them alone.
Various Scientology front groups - management services, etc. - do counseling and collect "withholds," and I've seen an actual letter from WISE (World Institute of Scientology Enterprises) which threatened a dentist that it would make known to the IRS the dentist's non payment of taxable income, unless the dentist kept his mouth shut and did not create problems for Scientology.
Remember that Hubbard was reporting "Communists" to the FBI as early as 1951 and, IIRC, reported a Mission holder (Alan Walter) to the IRS in the late 1960s.
Scientology playing footsies with the government is nothing new.