Unfortunately, reality is not determined by what you personally don't believe for a second.

Evidence (the Commander in Chief calling the opposition terrorists, and celebrating their government executions, for example) indicates that reality indeed reflects the things you personally don't believe.

Trump sees many Americans as adversaries (i.e. the 'radical left' like Alex Pretti an ER nurse and Renee Nicole Good - a mother). In his first term he asked whether protestors can be shot in the legs.

So in short it doesn't matter what the Pentagon thinks as Trump is the commander in chief and as far as I know the Pentagon has to follow his orders.