The problem with this case is that it was an intel led operation and not someone actively waving a weapon around.
With intel led operations, you can only make decisions based on the information you have. The intel could have been sound, and he may have actually been a threat, but to reveal operational intel or sources of intel could have put further lives at risk.
I'm not excusing the lies or the subsequent cover-up, I am just stating that their may have been genuine national security implications at play.