TNG itself is a little unclear on this point, as Troi had to take a test to become qualified as a bridge officer, but during "Disaster" is deferred to by the far more qualified (in military terms) Ro and O'Brien
A clearly unqualified Troi taking charge in "Disaster" was silly.
Actually, IMHO, the interaction there is rather different from "Troi takes charge"...
Essentially, Ro takes the initiative and performs a risky engineering procedure that makes O'Brien go apeshit. O'Brien tries to take command because engineering is his field of expertise, at which point Troi cleverly begins to interfere, in all innocence asking Ro what's going on - thus making herself the alpha female, because she's asking Ro to give her a status report (however informally).
Cut to the next scene were Ro (technically in command) and O'Brien continue to bicker about engineering decisions. Troi asks "What do you suggest?", at which point O'Brien starts to brownnose her, calling her "Sir" over Ro's not-quite-dead-yet body. That gives Troi the opening to do the humane thing and stop Ro from killing everybody in the secondary hull; she tells O'Brien to proceed, a not-quite-command which O'Brien eagerly takes for command with an enthusiastic "Yes, Sir!". Yet Ro continues to offer alternate ideas and act regardless of Troi's recommendations; to her, Troi is just "Counselor" throughout the exchange, not a superior officer.
Cut to the third scene. This is where Troi first indicates she "is" in charge; she dresses down Ro for her latest infarction, and even gets a rare "Sir" out of her. But not when giving her a direct order; it's back to "Counselor" there. It remains completely open whether Ro would really hold back ship separation just because Troi tells her to, and unlikely that Ro would consider her a superior officer.
I don't see Troi being in command there, either by protocol or by winner-of-pissing-contest authority. Instead, she is in control
-thanks to the insidious ways of an experienced empath, one who knows how to best play the two hotheads against each other and make the superior officer (Ro) do the right thing as defined by the superior engineer (O'Brien).