Agreed. This is how I took it, too.
I usually catch on to twists, but damn, they got me, because: Jason Ritter. I hated seeing him turn into the "nice guy" but good job, he had me fooled before. I wasn't expecting him to be the big bad, either, but I should have, since he was there, and didn't seem to be showing signs of anything. The people at Biona ended up really wanting to help, and the one guy they trusted, was the murderous asshole.
I had been hoping that the people were somehow in an alternate universe, or something, so that Dion could get his dad back, and Nicole could have her husband back. Dion was so sweet, wanting to protect his mother, and try to heal Pat.