A doctor cannot take lead in a crisis, rank notwithstanding.
Apparently she can, see "Descent". She might not be first choice, and ranks below all the regular senior officers in the line of command, but Bev seems to be considered more suitable for the command than dozens of Lt. and even Lt. Cmdr. officers who are wandering around the Enterprise!
Of course the real reason is she is a regular character, and it is a TV show, but we are just messing!
Worf over Geordi made sense due to the fact that somebody had to man the engines.
Someone needed to man tactical as well, but it is fair to assume Worf was more disposable than Geordi. Geordi must be a very nice guy though because in his place, I'd be pissed at being passed over for a mere Lt.