I still say Tony crossed a line that Jack would never cross.
Sure, he might have, but then again up to this season we haven't ever seen a line Jack wouldn't cross to protect the USA. Heck, how many times has Jack risked lots of lives (many more then what Tony threatened) in some crazy gambit that just luckily pays off.
I can't remember the season, but didn't Jack give back the very item (that season version of the CiP) to the bad guys after spending half a season to get it, in order to track it back to the main bad guys? Didn't he have to get permission of the President and vow that nothing would go wrong with his plan, because if it did thousands upon thousands of people could die? And, if I remember correctly, it did get loose and it was only by getting lucky he was able to recover the item and prevent lots of deaths (and catch the big bad). All that risk to thousands of people just to catch the bad guys.
That's basically what Tony was doing. Risking a lot to catch the bad guys.
Up until this season Jack would have been right there along side him doing it. The only difference is that this is Jack's show, so if Jack had been helping Tony all along then things would have gone smoother for the innocent civilians and a lot worse for Tony and Jack and their friends and family.