Supervisors were correct on the policy but perhaps they could have provided nicer customer service when explaining it and perhaps even let the existing seat assignments remain.
Unfortunately it was up to the OP to know the policy was that they were only entitled to extra legroom benefit when they were all in the same reservation and that by splitting the records any computer sweep could boot the kids out of their enhanced seats. (Note this is not unique to AA, similar things could happen on UA as well). Therefore the Flyertalk conventional wisdom is not to call and bring attention to your reservation. A better solution (if this happens in the future) is to keep the 2 aisle seats and then during boarding see if the someone in the middle seats of one of the 2 rows would swap (unless they are both companions of the window seat - your odds of people switching a middle to are very high).
So, OP I would say its a tough lesson to learn and it would have been better if you had a more sympathetic ear from AA so even though technically they were right they ultimately lost in your mind based on their methods.