How was John Connor damaged in Terminator Genisys?

Question

SPOILER ALERT: Do not read this if you want to wait to see the movie first.

At the end of Terminator Genisys,

Pops pushes John Connor inside some sort of gyroscope thing which would seem to pull John Connor apart. This was happening at the same time that the entire complex was blowing up.

The gyroscope thing looked like

the time machine they used at the beginning of the movie, but Pops said that Skynet did not have the ability to send a person through time in the apparatus yet. So what was happening when it seemed that John Connor was being pulled apart by the gyroscope thing? Is the time machine really a big magnet? How does it work?

Also note that

it did not actually kill John Connor, as shown in the bonus scene that you see if you sit through the credits. So perhaps the gyroscope thing actually protected John Connor during the explosion. How does it work?

Answer 1

At the start of the movie

when the humans are figuring out how to use the time machine to send Reese back, one of the techs explains that the field will destroy anything metal and says something like "imagine tin foil in a microwave but a zillion times worse."

Then you have to assume

that the part of the time machine they had completed was enough to cause the huge reaction/explosion when the nano-metallic John Connor was in it.

As for your mention of the post-credits scene, unless there was a second scene after all the credits (I saw one part-way through the credits):

It wasn't John that survived, it was Skynet, as represented by the sphere and holographic "person."

Answer 2

We know the time machine cannot send non-living things back unless they are covered in living tissue or similar."Kyle: You go naked. Something about the field generated by a living organism. Nothing dead will go." As we know, John Connor is currently is not replicating his human appearance in the final moments of the fight. Most likely, the T-3000 is able to replicate living tissue similar to how the T-1000 can and did this when being sent back the first time, so him not doing that now in what equates to probably a giant magnet would cause him to be shredded to bits if in there long enough, hence why Pops was holding him there.
The bonus scene was of Genisys underground showing that it isn't quite dead, if I'm not mistaken.

Answer 3

According to CinemaBlend:

But those who wait around for the scene after the credits know that not all is really well in this new timeline, as Genisys is actually still alive.

[...] The scene begins with a ball that is filled with red light and glowing – but then we see that it’s not alone. It turns out that Genisys – represented by a blue light in the shape of a child – has not been destroyed, and that the future of the robot uprising is still a very real thing.

They discussed the scene with the director:

It was always there as a kind of gateway - to further developments… It’s precisely a kind of, ‘it’s not over yet’ moment. On the one hand, it’s one of the things that points to there being further chapters. On the other hand, this is a kind of franchise where I don’t think anybody really believes that you’re going to end up neatly or happily. So, when our heroes drives off into the sunset and we think, well that went well. There’s still going to be a nagging feeling that wait, it’s not that easy.