Everyone involved in the production was very aware that people would see it as a tie to 9/11 but I don't understand what you mean by "feel a little embarrassed."
Poor choice of words, perhaps. I was on Day 3 of quitting smoking, too, so Bones, please forgive.
What I meant was, in real life the West bombed the hell out of a lot of people after 9/11, which was the crew's desire in the first few episodes of the season. Vengeance! However, in Enterprise they talked with their 'enemies,' and found out said 'enemies' (Xindi/Muslim world) weren't a monolithic group of bad guys as they'd been said to be. They really beat us over the head with this throughout Season 3 -- the Xindi being multiple species and so deeply factional was not exactly the subtlest writing ever. The thing that made Season 3 so different was that it showed us talking with those we perceived to be our enemies, instead of just escalating the conflict with them, and finding out that the majority of them were just frightened, but good people.
Of course, despite the engagement, the extremists (Reptilian/Insectoid/Al Qaeda) attacked us, but they were going to do that anyway. However, thanks to the engagement, the talking, these extremists were doing it alone, not backed by the rest of the people as they would've otherwise been. Without the diplomacy and engagement, the humans would've failed.
This was what should've been done in real life. Instead we got invasions and massive deaths of innocent civilians, which gave the world's real-life Dolims say to their people: "See? They're trying to KILL US ALL." It was very hard for a moderate Arab to argue with that when grinning American generals were on TV, discussing the "Shock And Awe" bombing that was producing piles of dead Iraqi civilians.
Blech, I really didn't want that to turn into an antiwar rant. I think, though, that Season 3 really did its best to show us there was a more human way of doing things.
I'll go away and be quiet now, at least until the end of this damn nicotine withdrawal reduces my propensity for idiocy and ranting