that's the obvious thought on how to solve this, problem is I don't think it's that simple. Not knowing the geography, alternate routes, number of people who may get disembark at the Fed facility from that bus, if any, etc...
In DC the Metro goes through a number of areas that are restricted, (Pentagon) and of course there is not an option to build a line a couple of hundred feet outside the area.
Just curious, are passengers on the Metro subject to ID checks or other security procedures if they aren't getting off at that stop?
In that case, the security checkpoint where people have to show ID is reached after the passengers disembark.
The level of bus traffic through the station is another issue -- every time security is enhanced above normal levels (e.g. last Inauguration Day), it creates a cascading bus backup (AFAIK, the bus passengers aren't checked, but vehicles are rerouted somewhat within the outer Pentagon complex). The only real solution is to reroute some of the buses to other Metrorail stops, but Metro is too hidebound (and too desirous of charging outer-NoVA commuters $3.00 for ferrying them on an "express" route to the Pentagon instead of getting only $1.35 to drop them off at the nearby stations at the southern end of the Metrorail system).