Verification of this individual's credientials is only part of the story. If I, or any one of us, is not comfortable with a situation, it is our obligation (both right, and responsibility) to handle that situation as we see fit. Even if the USSS agent was able to demonstrate the proper credentials and verification of those credentials was able to be obtained, it changes nothing.
A form 110A from the FAA is not a magic boarding pass, and neither are credentials with any other government service. Everyone must pass security, everyone is subject to inspection and verification (including crew), and ultimately, everyone is still subject to the authority of the Captain as Pilot in Command.
The details are still not fully clear, and will likely never be publically clear. We are in no position to judge, but we are in a position to support a pilot who exercised his right and responsibility as pilot in command to act in the interest of his company, his aircraft, and his passengers. Those who post that they would feel better with a secret service agent aboard miss the point; you'e not the captain. It matters very little what you feel as a prospective passenger; you don't carry the weight and responsibility as captain and pilot in command, and most importantly, you were not there, and haven't the facts to command in making such judgements.
FAR 91.11 specifically prohibits any person from threatening or intimidating a crewmember. While the facts are unclear, the use of a badge to intimidate a crewmember into allowing entry could be considered with the scope of the FAR to fall within the constrainets of 91.11, leaving lattitude to ultimately deny entry.
Let's not forget that some very notable assasinations were carried out by individuals holding high security clearances, and high positions in the government and military. Off the top of my head, I still have a very clear mental image of the murder of Anwar Sadat as he sat in the revew stand for his trusted troops. Because someone is trusted doesn't make them safe, and past checks assure nothing in the future. This is really beside the point, as the Captain was within his discretion. If there are other issues or apologies to be made, the company may do that after the fact. It's far better to apologise for having required the man to miss the flight, than to allow the man on board the flight if there is any question at all as to the safety of doing so. That's a matter of fact.
I can say this; I have delayed flights or taken actions in the past when I had an uncomfortable feeling about something, and haven't discovered until later the reason. Small things become big things. I've also had the unwise misfortune to disregard that little voice from time to time, and have come to deeply regret doing so shortly thereafter. Some years ago such a little discretion almost cost me my life in a parachute accident. I didn't feel quite right, but like the idiot I've too often proven myself to be, I went anyway, and very dearly paid a high price.
We're not just paid to drive airplanes. We're paid to make judgement calls, pure and simple.
Years ago I packed a parachute on a weekend, for a student jumper. Shortly after that I saw the same person enter the loft with a open reserve parachute in his arms. He had cut away his main, and had used his reserve. I was keenly interested in what had happened, and his actions. As I listened to his account, it was clear to me that he had no need to cut away from that parachute. He made a conservative decision, based on the moment and some degree of inexperience, and it worked successfully for him
At the time, I had a little pride and personal feeling tied into the issue. I wanted to make it known that my pack job hadn't caused this situation. A jumpmaster pulled me aside, and asked me to say nothing. I attempted to say something, but was held back. I was reminded that regardless of the correctness of that student's decision, it had been made, and it worked. He didn't have to cut away, but he did, and he handled it well, and lived. If I tried to confuse the issue by telling him he did the wrong thing, then the next time he were to have a real emergency up there, he might become confused, freeze up. It could cost him his life. I understood, and kept silent.
This captain made a call. Perhaps the USSS agent presented no danger, perhaps not. Perhaps he copped an attitude, or showed discrepancies in his boarding paperwork. Regardless, the Captain made a decision based on his judgement and experience, and the worst that happened was one passenger had to take a different flight. NOT a big deal. Don't second guess the man. Not one of us were there. How can we do so? He made a judgement call, and nobody got hurt. In my book, that's probably a good call. It's far better to make a conservative judgement decision and not need it, than hold back, and realize it's too late.
Let the man live. He's doing his job.