The reason the seats left were scattered is because of people checking in online. That can be done up to 24 hours ahead. And as such, this is not something that would be unique to AirTran. But at the same time, keep it in mind in the future as an option.
Since you were not given a seating option ahead of time, I'm guessing you must have booked through an online agency or a regular travel agent. The airline's own site will always give you the option of choosing seats.
Ultimately they are not going to let you sit apart from the kids. The reason they have you check at the gate is because they have to page other passengers to switch seats with and give them their new seat assignments as well.
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