There was always more to the facility than meets the eye, that was stated in the opening document. His last note was that he defeated whatever it was and he was going home, dead or alive. It ended up dead. I may be reading your post incorrectly, but those soldiers were Murkoff security and they repossessed the facility when shit hit the fan, there are a few documents about it.
It's open ended, yeah, but Miles' story is finished. He became a vessel and then was killed. There's no way Murkoff would let that story out of there, although that may be out of their hands now.
I thoroughly enjoyed it! The outdoor section was incredible, and the tension throughout the game was pretty amazing. Towards the end the game seemed to be less relentless, but at least it was gorgeous to look at.