Which actually makes it worse because SF already knew of situations where the CO was unavailable due to various circumstances (ala Voyager) and the EMH was the only one left onboard that could deal with the situation at hand.
I was actually hoping that holo Janeway was programmed for such eventualities in case the CO wasn't available (for whatever reason)... in which case, she could assume temporary command (much like the EMH did).
I mean, the VOY crew was able to pull it off in the field... so I don't see the issue with this being the case with Holo Janeway when SF was programming her - but as you say, the way the shows are written, they make SF look very incompetent.
They could have still limited her programming to a degree if they were worried about her going rogue for whatever reason, but otherwise, I don't see a problem in giving her the ability to become solid or permeable to matter interaction (aka people) so she could conduct some maintenance other automation can't or wasn't programmed for, and help defend the ship at the very least against intruders.
She'd be able to take on Drednok with relative ease.