Yes, I know very well what traveling with my kids is like. Have done it countless times, all over the world. Have not had any problems, even when they were lap infants. The "magic line" was crossed in this case twice, I think, and not a single time by either of the children.
You're not alone. Many of us have. My first-born had visited every (inhabited) continent before he turned 2. And all of his intercontinental flying was in J. And he was an angel---almost all the time. Except that one flight from SCL to IPC when he had a bad head cold and couldn't be consoled.
What we learned, as I'm sure you have, is that every trip is different. Just because it has always worked in the past doesn't mean it will in the future. In this case, clearly your kids had some issues that required multiple parents' hands. I'm not blaming you, but as a parent you must know this happens from time to time.
All I (and several other posters) are trying to say is splitting the family is a calculated risk. This time you rolled craps. Yes, the FAs could have been more accommodating, but, as
Thomas Hudson put it, there is blame to go around here.