It wouldn't be rude, IMO, to continue to shop as long as you don't interfere with other's observance of the moment of silence.
People may have a reason not to observe the moment of silence. Maybe they are protesting the military in general, maybe they are protesting a particular war or peace keeping mission, maybe they aren't native to the country and don't observe the moment of silence because they don't know anyone involved in any of the major world conflicts. And that is their right.
As long as they don't interfere with others, the way the father in the 'A Pittance of Time' video did, they're not rude. It would mean that they would have to wait, quietly, in the checkout line if they just happened to get there at 11:00 when the observance of the two minutes of silence was announced, though.
In the OP's case, I think there was an obvious glitch with the system. She did her observance the first time. It may or may not have been right at 11:00 that she did it but she was fine to carry on when the PA system seemed to be glitching.