Would you have let Bodhi go?
Think about it.
Bodhi murdered a heroic off duty police officer in cold blood,who was outmanned and outgunned. His reckless decision to greedily rob the bank vault led to the death of Grommet. His refusal to turn himself in at the airport put Nathanial and Roach in mortal danger. He threw Roach to his death, when he should have taken him to a hospital. His associate murdered Pappas. He kidnapped Tyler and would have had her murdered had Johnny not agreed to assist in the bank robbery. He coerced an FBI agent into commiting a felony.
By letting Bodhi go, Johnny allowed him to get away with all of the above. Plus, did Johnny lose his career? I'm sure Tyler and him were married at that point and he needed to put food on the table and pay the bills. Both of which will be jeopardized when other law enforcement personnel clearly saw him let Bodhi go.
Come to think of it, would Johnny serve prison time for that? I think he would be fired, or forced to resign at the very least.