Filling over an etch probably won't work as it isn't usually deep enough to hold the glue.
If you are looking for a topical barrier to prevent anything acidic interacting with the calcium in the marble (whichis the cause of etching) you can use a wax but it will be a maintenance issue - you will have to do it occasionally just like when you wax a car.
The more use the counter gets the more frequent you will have to do it.
You can find the waxes here:
http://www.defusco.com/Waxes-Other-Stone-TreatmentsGlad to be of service,
Mark