By PHILIP TAUBMAN N.Y. Times News Service WASHINGTON — Dissent is not a popular commodity in the Federal government. The bureaucracy has developed numerous and sometimes Draconian ways of stifling differences of opinion and unconventional thinking.When J. Edgar Hoover ran the Federal Bureau of Investigation, agents who challenged his policies were transferred to Missoula, Mont. At other agencies today, timidity and insularity are defended by banishing dissenters to shuffling paper, indefinitely postponing promotions or inserting negative information in personnel files.