Personally, I lean Stark myself, but there is one sticking point that really irks me: the lack of a "pardon before permission" provision. An accord as well built as the Sokovia Accords were implied to be should consider the fact that, when faced with critical situations involving limited time and/or active obstruction, an Accord hero should be able to the act with the expectation that an after-action investigation would judge if the actions taken were justified and the appropriate punishment for disobeying orders. Given that both the World Commission (Avengers 1 and Agents of SHIELD) and SHIELD have both been corrupted in recent history, such consideration should be mandatory.

I.e. "General Ross was overtly impeding an active investigation, disregarding new evidence, and threatening Accord-compliant heroes without sufficient justification (the previous encounter said heroes were involved in, though not entirely successful, was handled in a proper manner to minimize loss of life and collateral damage). The evidence at hand presented a clear and present danger that required immediate investigation and resolution. Ensuing damage was limited to an abandoned Hydra facility and personal materiel. Stark broke compliance only in resorting to lethal force based on personal grievance and should be sentenced accordingly. Other agents involved have been found non-compliant, but acting in good faith and should be sentenced accordingly."

Given that Stark was stunned to find them imprisoned at the Raft, and was openly attempting to retroactively resolve the Winter Soldier incident, he very likely assumed such a provision had been included. Indeed, maybe it had, and Ross was just that far off the reservation in his response. We'll never know, however, because Cap broke 'em all out before any justice beyond initial containment could be pursued.

It's worth noting that Stark references his own misdeeds in defending the Accords, pointing out that Ultron happened while Tony had no oversight and that such oversight could have avoided the calamity that followed. Stark has a defined pattern of making mistakes, learning from them, and doing better in the future.