I know nothing about the people involved in this so my comments are general, not specific.
I has been my observation that rising in a police bureaucracy (or any other bureaucracy) requires that one be very attuned to the realities created by the bureaucracy. The world inside a bureaucracy does not always resemble the world outside of the walls. Most cannot handle this level of cognitive dissonance.
The other possible explanation is a naive belief in the truth but without an understanding of the unique dynamics of this particular situation. A complete lack of experience in events likes these can really make for some big screwups. There is also an arguably cynical position that no matter what is done, the PD will be painted in a bad light, so why bother. I doubt that anyone in that department would handle things the same way if we rebooted back to the day of the shooting.