It doesn't exonerate Captain Rogers, nor can it explain why his crew was seemingly unable to read the information that was staring them in the face, specifically the fact that the aircraft was climbing the entire time they tracked it. That flight profile screams "NOT A THREAT" to anyone versed in anti air warfare, which you would expect the crew of an air defense cruiser to be, yet somehow they reported the contact as descending on an attack vector. There were doubtless many reasons for this failure, combat stress, the newness (at the time) of the AEGIS combat system, the double IFF response, the failure to establish communications with Iran Air 655, and so on. None of those facts excuse the failure though, at the end of the day the Captain of a ship is responsible for the happenings aboard ship, whether he could have influenced them or not, and Captain Rogers certainly had control over the training of his crew.
I seem to recall stories at the time of the shoot-down that the F-14s operating from the dual-use airbase Flight 655 took off from would routinely set their IFF transponders to Mode III (Civilian). If the crew of the Vincennes was aware of that then the IFF response from Flight 655 would have looked no different from an F-14.
This doesn't excuse Capt. Rogers since the flight profile and heading were, as you say, non-threatening, but it does remove a useful piece of information that might have led to a different decision.
