The ruler is always free to ignore the marshal. You won't go seeing the judge fine the ruler if he doesn't obey the marshal's commands.
You could say the same for rulers having an estate in a region of some lowly knight. And yet it won't happen, because there are also game-mechanics that equal "obeying". For example, combat settings. The marshal
does tell the ruler where on the battlefield to stand.
Being part of an army shouldn't be considered being subjugated to its marshal.
Err, what???
It doesn't get much more subjugated than being subject to military commands by someone.
For gameplay's sake, I would request that rulers not be given a restriction for this. Rulers have many duties as it is, we shouldn't ask them to figure out military affairs themselves as well, on top of the diplomacy they must do.
He can always, you know, not be in any army.