I think there is something much cooler about a memorial flight in the MA verse a SEA. Even those of us who don't care about score probably see the MA as a larger level of significance. The perks count, the deaths count, how cool was it to see a 262 flying formation with enemy aircraft!?
IF you're going to do it in the MA, you have to accept it for what it is. Although I think it's very disrespectful and more than likely just immaturity, I don't think HTC should change the rules for memorial flights in the MA, that kind of takes away from the point. I certainly don't want to effect those players who just choose not to participate, I have no negative feelings towards them and do not want to force them to follow different rules because of a memorial flight.
Back to the OP, I don't think knowledge of the memorial flight was the issue, and I don't think HTC should be required to go out of their way for these things, unless they choose to. I think VEGA's flight went pretty well, especially for the fact that hundreds of people participated.