I think it is a shame this thread has suddenly become so angry. As a selfish child-less traveler I dread a crying baby being near me on even a short flight. But the more generous side of me can see straight away how difficult it must be to be a family split up a long way apart in the aircraft. I would have hoped that an airline, when changing aircraft type, would be more active in managing this issue.
The cabin crew could have asked passengers in the row behind the bulkhead row to move since these are not particularly special seats and having one's partner one row behind must be better than many more rows behind.
And just because the OP didn't understand the baggage rules and was frustrated by another apparent obstacle in their way doesn't justify unpleasantness here. I'm sure they were thankful to the supervisor and check in agent when the fees were waived, even if they didn't express that here!