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Just using the mass drivers as pea shooters to wipe out the stubborn parts of the Narn resistance without destroying their economy or biosphere. Glassing them from orbit is easy, controlling their planet and making them a productive member of society is the tricky part. :-)
Prolonged use of unconventional weapons could be very detrimental to your galactic image, (not that its a very good one at the moment).
Couldn't you just use the main guns on your ships to bLast deep holes in the bunkers? Unless they're very very deep, or under a good deal of water, in which case use depth charges of some sort, or seal 'em off underground by burying the entrances under rubble.
Very few should require a mass driver to destroy.