Presumably, Starfleet equips starships with self-destruct routines because they believe there are circumstances in which it is necessary and expected. Surely, then, every case of using the self-destruct sequence couldn't automatically carry a penalty for the commanding officer. How can you penalize someone for doing what they're supposed to do?
Which might be why Picard fell under suspicion: he did not destroy his ship!
Perhaps when Philippa Louvois insisted that a court martial is standard procedure when a ship is "lost", she was referring to situations where a ship's whereabouts become unknown? There is no need for the procedure if a ship is "destroyed" or "decommissioned", but a ship being "lost" (that is, "misplaced") is exotic enough to warrant inquiry.
On the other hand, nowhere in Star Trek do we get the impression that the abandoning of a ship should
be followed by scuttling. Picard was found innocent of wrongdoing or negligence even though he didn't scuttle, after all. Quite possibly, the self-destruct machinery is in place solely for tactical applications, such as the ones where Kirk or Janeway took their enemies with the scuttled ship, or threatened to do so.
Picard lost two ships from under him, and always got a new command. Sisko lost one (not counting, say, the time he lost her to boarding attack but got her back eventually) and got a replacement command, and never mind all the runabouts he went through. So even if we lack precedent, we got plenty of postdecent for loss of command being no grounds for blocking further command.