Whether or not Connor is consciously aware that his likeness is going to be used does not change the fact that it would be in that situation. In terms of the paradox there is no difference between Marcus taking on Connors appearance of his own accord or Connor telling him to. If you want to say that intent does make a difference though, then you already have an out as Kyle Reese never knew he was John Connors father. I think it's best not to think about it too much, the first movie actually handled the paradox the best as it was a true straight up self contained paradox.
Finally got around to seeing this tonight. Great summer movie. It's got flaws, for sure, but it was a fun movie to watch. Very much so, IMHO. That was obvious CGI work combined with some live action of Bale. It reminded me of the 360-around-Tom Cruises-car shot in War of the Worlds, only way, way better. I loved the creepy WotW-sounding giant terminator (that whole scene had that WotW vibe), but hated the "Transformenatorcyles" that sprouted out of its legs. Too hokey. Great nods to the the first two movies, especially the Arniebot's reaction to getting clocked upside the head. And Mrs. Connor must be one helluva doc, performing a heart transplant in the desert like that! I hope there are still stocks of anti-rejection drugs that her husband can take. Oh, and with all the great CGI stuff throughout the film, why did the last shot of the helicopters flying away look so shitty? Didn't look remotely realistic to me.
From a layman's perspective, it seems to me as if it is one continuous shot ala Goodfellas. It looked seamless from the time Bale ran into the chopper, took off and it crash landed... all while changing perspectives! Good piece of technical work there, IMHO.
IMHO, it was a combination of live action with blue screen and CGI. I just don't think some of the angles and moves they had are possible with an actual camera. I'm really hoping that there's a making of/behind the scenes bit on the DVD/BlueRay releases showing how they did that sequence. It was really cool.