Then again, if the ship were allowed to be a coward, she wouldn't be much of a warship...
In some matters the ship outranks the crew, being able to impose safety measures and give answers to questions not asked. On the big decisions, she has to bow to the commanding officer. And most of the heroes can override the mediumweight decisions of the ship, too, as they are important department heads all, with clearances and codes and whatnot - hence the all too common "safeties off" as a cause of injury in Crusher's reports, and no doubt McCoy's too.
On the issue of who gets to decide whether doors (the cabin ones) open or not, the interesting question is whether this matters. Khan can force a locked door open with his fingertips. Quinn can throw people through closed doors. The doors are not airtight, with light shining through the crack underneath. And people leave doors ajar for eavesdroppers anyway...
Timo Saloniemi