Yes, it might not be a SHIELD facility on the books, but at the very least, it's a facility that SHIELD oversees/uses for it's more "experimental" medical procedures. Killing the two guards was absurd. If I was Fury and heard about this fiasco, I'm shooting the Bus right out of the sky. Even if they later explain that it was the base of some nefarious/evil organization so that Coulson and team's actions will retroactively seem less sociopathic or insane, doesn't make it less so in the moment, since based on the information at hand, the obvious assumption is that the base is aligned with SHIELD. Attacking it is basically a declaration of war against his own organization. Just frustratingly poor writing on this front.
Especially frustrating because there was so much cool stuff in there... the (probably) Kree, Garrett, Trip (despite not having much to do), the midair docking sequence, the most advanced database querying system known to man, etc.