There were two categories to the misbehaviors - the airplane making in the pews and the crying and wailing at the baptismal font.
The airplane incident was visually disruptive. If young children can't be calmed down with a snack, a book, something that is done discretely, then they can be removed from the premises by a nanny who was brought for that purpose. Nikolai and Felix don't need nannies to remove them, but should not be encouraged by adults to continue with those actions.
The crying at the baptismal font, totally interrupted the service, but was done by a very young child who obviously didn't know what was going on, and that her mother was busy with another obligation at the time. She should have been removed at her first resistance to stay where she didn't belong - and the noise she created later was not amusing.
I feel for Marie and, particularly, Joachim, to whom this service and this baby is so symbolic of a new life for him. I think it was total disrespect to allow Isabella to wail away as the bishop continued with the christening. She was not crying in the back of the church somewhere, but right at the font. Totally wrong, not cute, whether it involves royal parents or any parents.