All the studies so far indicate sitting (or other forms of inactivity) are bad no matter how much you exercise at other times.
The best natural experiment was the London bus driver study which showed huge differences in heart problems between drivers (sitting all day) and conductors (standing all day). Both were drawn from the same pool of employees and randomly assigned roles, so the experiment was naturally controlled for everything except the difference in behavior.
There were some other differences such as drivers having a more stressful job and conductors having more social interactions which might explain some of the differences in outcomes apart from the sitting/moving difference. But in any case, sitting for hours a day at a stressful job with minimal social interaction is incredibly bad for your health. Programmers take note!