Yes, a lot of them ultimately perished in horrible ways, but they saw a shine, presumably from that giant obelisk and were transported to a safer version of that planet in some ascended realm.

Their bodies were reanimated along with the shuttle to give closure to the team so they could move on, however these...obelisk aliens...while trying to do the right thing could only bring them back while they succumbed to their planetary fates regardless.

There is just something in the way that Dr. Caine assures T.J. that the crew will find away home one day, it's not a case of maybes, the people in that cabin know things work out in the grand scheme but much like the ascended ancients of SG-1 have a non-interference policy.

Of course he sends T.J. back, and then we get a whole other situation with the Novus people, who themselves (outside of that small colony) have mysteriously disappeared into thin air.

Then there is a whole other discussion about T.J.'s unborn child, if the obelisk/cabin reality situation is real, that baby...also has to be real, making her effectively some kind of human/ascended obelisk alien hybrid.

There is definitely a lot more to the cabin scene that meets the eye, I've been thinking about this scene a lot on rewatches.

I've watched this scene dozens of times, and I can say for sure it is not a dream, or a vision. Dr. Caine ascended with the rest of the Eden planet team.