I sort of lost interest over the last year or so as some of the episodes were just plain bad and so predictable. The writers seemed to be on remote control for a while but this episode while not sold on the concept was at least interesting and of course a two parter to create more drama.
Is John and Zelenka to die, I doubt it, somehow they will survive with the Asgar or someone beaming them out in the nick of time. As for the end game machine, come on now if it blew up stargates in 3 days before why did it do it now in less than an hour.
And the ships blowing up as they enter the hyperspace window and you can see it is in my opinion just hogwash, the window would open then as the window closes the hyperdrive would be undone and no one would ever know. But then that would not make for good TV.