Mujib was an actual traitor; he began talks with India for an independent Bangladesh during the 1960's, the conspiracy was detected by the intelligence, but they were ridiculed when the conspiracy was brought to light. The case and evidence files were burned (likely strategically) during riots targeting government buildings and the case was eventually withdrawn after intense pressure. In 2010, the conspirators admitted in Bangladeshi parliament to the historicity of the conspiracy.
en.wikipedia.org
However, that wasn't even the main reason why the military would not allow Mujib to become the Head of State, the main issue was his 6 point plan which would have relegated the federal government to defense and foreign affairs only, a dangerous level of decentralization which would have opened the path for Pakistan's disintegration, the plan also called for separate currencies, foreign exchanges and militaries.
Pakistan and Bangladesh should not have never been under one state and separation was inevitable given the differences.