If there's been even an unpublicized consideration of the possibility of infection by the aliens, the first consideration upon the landing of an alien craft would be a quarantine. Not for concern of the lives of the locally affected civilians, but of the populace in general. So any indigenous military forces would be bent to the task of establishing a perimeter and enforcing a kill-zone around the site. The aliens aren't engaged in a ground invasion; they aren't going to stray from their landing site. The kill-zone would be intended to prevent humans from leaving quarantine.
Military forces would notify PHALANX of the presence of an alien ground force, and maintain surveillance on the site through satellite, aerial and ground recon presence. At the first sign of the aliens attempting to pack up human prisoners or leave the site themselves, the local national military would call in a strike to destroy the site with heavy conventional or nuclear weapons.
PHALANX would come on site, restrain any local human presence with a less-than-lethal response, and kill or capture the alien ground force. Upon mission completion, any humans or aliens would be returned to a secure processing facility. Humans would have to be carefully screened for biological or technological contaminants before being released. Aliens, of course, are taken to Guantanamo for water-boarding.
In the event of a PHALANX mission failure, or of an alien evacuation, the penalty will be the destruction of the area by our own forces, leaving it unlivable.
At least, this would make the most sense to me.
