No way Tony's not a "bad guy." Shooting federal agents in cold blood wouldn't have been necessary as Jack has shown in the past. However, 24 has always seemed to make a point of how some people can have a skewed sense of what needs to be done in order to achieve the final goal. Dubaku (sp?) caused the death of the people in the planes, but in his mind he was doing what needed to be done for his country. Right wrong or indifferent, that's the perception presented. Jonas felt that casualties were acceptable if it resulted in the country taking a more aggressive approach to security. Hell, even the prez's daughter (who I absolutely hate, both in character and attitude) may wind up screwing up the deal with Jonas. All season the focus has been on who is to say what level of violence is acceptable - torture, murder, mass murder.
There is no way in Hell, that an administration has a brat like the prez's daughter being the sole advisor to the POTUS. The entire time she was arguing with Mom about making a deal with Jonas, I'm thinking "Umm, she took an oath swearing the health and welfare of this country would be her primary goal over everything else - including revenge for a murdered son." Geez, I guess the Joint Chiefs were too busy reaming the guy who questioned a direct order from the CIC. "Uh, ma'am are you sure you want me to abort the fighter strike?"
Sorry for the rant, but it bothers me to see the writers resort to plot devices that rely on incompetence at the executive level.
BTW, it just seems to me that they're setting up something with JG. I don't know what it is but every scene with her just makes me think she's about to do or reveal something that'll be devastating. We'll see..