Well, my guess was right that the regular Earth Superboy was going to bite the big one. Psycho Pirate also bit the big one by the hands of Black Adam once he was released from the vibrational machine. It's unknown whether Superboy Prime lived through the destruction of the machine, but the preview on the last page for next issue says something related to whether Prime can be stopped or not.
My guess is by the end of Infinite Crisis #7 everyone who knew about the multiverse before Crisis on Infinite Earths will be dead minus Power Girl. This means Alexander Luthor and Superboy Prime will be dead (if they're not dead already, although I believe Prime is still alive, we never really saw where Alex went to before the destruction of the machine). This also means Earth-2 Superman will be dead as well and he will probably be the one to kill Prime, which goes against his beliefs when IC began. He'll realize the only way for there to be a resolution is for Superboy Prime to die and he'll handle it himself.
Conner Kent's death was a bit of a cop out and his death doesn't equal Supergirl or Barry Allen's death in COIE. I've never been a big fan of Superboy, especially when he was born after the death of Superman as a genetic combination of Superman and Lex Luthor. It's also a bit of a cop out if you read Teen Titans this week, the first one year later chapter for that book. At the end Robin is seen as trying to recreate Conner with Superman and Luthor's genetic material. I believe he is on his 96th try (don't have the issue in front of me at the moment) and all have failed, but he continues to try. Geoff Johns is writing Teen Titans, so we should not be surprised that it would tie into IC and the upcoming 52 pretty tightly.
One thing that caught me a bit off guard is that Superboy Prime said the Flashes tied him up by a red sun for years. He doesn't explain whether the Flashes watched him during this time or anything, but he escaped and built a suit (that looks Anti-Monitor like) to give him continual yellow sun energy. The problem is that it was a known fact that Prime was not vulnerable to the red sun like the modern day Superman is, so I don't know how the Flashes kept him at bay for years using just that. It was also funny to see Prime say that Black Adam's punches only tickled and he joked about a weakness to magic.
The next one should be exciting and hopefully 52 will be exciting as well. It's a good time to be a comic book reader.