Good point. It seems Kirk didn't need a separate Science Officer because his XO performed the duty; Janeway being both CO and SO doesn't appear out of line with that. Was Riker a slacker for only holding a single job? Was Picard his own SO?
Chief of Helm probably wouldn't have been among the mysterious high-rankers, or competition with Cavit would have been an issue. If Lieutenant Stadi held that position, then Tom inheriting it becomes rather logical. Also, a department head at the bridge during the Maquis hunt is sensible as well.
Chief of Ops would probably hold lower rank than Cavit, too, because Ops folks appear cross-trained and command-qualified elsewhere and would have offered unwelcome competition again. A Lieutenant in command of the Ops department would make a lot of sense, though, and Kim inheriting his or her position is IMHO a bit more attractive an idea than Janeway having such a junior (really, basically fresh out of the Academy) officer as a department head.
OTOH, the Ops Chief might not have been as crucially needed on the bridge during the Maquis hunt; he or she might only have been awakened for the actual intercept (and thus essentially ended up dying in his or her sleep), whereas the top Conn officer would be constantly needed while navigating through the Badlands.
What other departments should we consider? Janeway mentions that there are thirteen of them reporting to Tuvok, in "Scientific Method". Which would warrant the sort of chiefs that could explain away the high-rank casualties but wouldn't compete with Cavit?
To confuse matters, "Good Shepherd" has an Okudagram mentioning a couple of categories coinciding with the known names of Divisions: say, Command and Engineering. Each of these encompasses things we know to be Departments: say, Ops, Conn and Tactical are listed under the Command title. But the list of sub-categories can't be the list of the thirteen Departments aboard the hero ship, as there are in fact 21 sub-categories listed! And that's for just three Divisions, while dialogue elsewhere speaks of several other Divisions.
Perhaps Tuvok has 13 out of 29 department heads report daily, as Janeway says, while others only report once in a blue moon?