Are the survivers clones/aliens/hybrids or dead ?

My take is the aliens felt bad for taking their lives, so they repaired them physically, but also took part of their physical appearance so they themselves could experience a higher form of being. From the sludge-like, seemingly 2 dimensional existence to a 3 dimensional form.

They copied Whitney because it was his selflessness that kept him going. Then having learned from the 'real' alpha the alien brought them back. Notice only the team lived and not the miners or the researcher that killed the captain. Not sure why that worked the way it did though.