Poeple that stand on etiquette in this way often have inflated ego's. Not a trait I would welcome in any aikidoka.
To me etiquette is useful in setting a social context of training which has at its core respect for each other. I am sure you did not do the bowing ting out of disrespect. Your teacher should respect the fact that you did not know you were doing anything wrong. And as for the wrongness...if you had flipped him the bird or had dropped trou, I guess he would be right.
As for getting on your knees for people....perhaps in some contexts, walks of life and/or professions that is the way to go.
As for Aikido, anybody getting on his or her knees for me in the context of training session I ask to get up asap and start training.