Was the apology necessary? Was it rude to close down the city, even though they had permits, etc?
As others have said, whether the apology was necessary or not is less important than the fact that it might be a good idea on several levels.
I can't say 100% whether closing down parts of the city was rude or not, but I will say that just because they had permits doesn't make it non-rude. Many, many things that are perfectly legal are also rude, and a government office giving you permission to disrupt someone's livelihood to further your own does seem to fall squarely on the "Yeah, that might be rude if you don't handle it well" side of things in my opinion. For this specific case, though, I don't know enough to judge.
I do have one example of possible rudeness due to filming in Boston. Back in the 90's there was a movie about a mad bomber loose in Boston. Blown Away, that was it. They filmed all over the city, but it's not like everyone knew what was going on at the time. A friend of mine was walking through Copley Square and noticed there was a big hubbub with lots of cop cars at the opposite corner. This is not a common thing but also not completely unheard of, so he didn't think anything of it. Until a paddywagon exploded, which scared the snot out of him until he finally noticed the film crews and equipment. I'm sure they did everything they could to warn people in the area, but this is an area they simply couldn't close off and that's full of people moving from one point to another. So were they rude to essentially stage a terrorist attack in the middle of a busy city? I don't know, but I do know my attitude would be different if they did this now rather than back in '91 or so.