I don't what those options are but I think it's inappropriate to give a Hashgacha on a Jewish establishment open Shabbos.
Thats why there are no mehadrin food store in Ben Gurion airport.
But technically when your trying to certify kosher food where do you draw the line? If the waitress are dressed inappropriate is that a hashgacha issue? If the place is a hangout, has bad music, is that a reason to pull the hechsher? Unless the place is making chometz on pesach the food is technically kosher even if they are open on shabbos. So unless there are better options available some out of town Hashgachos feel its better to have kosher food available to the general public then to be machmir on other principles.
The shomer shabbos customers on the other hand should definitely be looking for shomer shabbos establishments with tznius waiterss etc to buy their food.