You have valid points.
Don't you believe too, that SWA as the company purchasing AirTran had the right to participate. If I purchased another company I kinda feel like I should have that right as well. After all it is their money, right? Personally I think they should do what they want and if they felt there own employees should not have their seniority decided by an unknown person then that is SWA's right to do so.
My only heartburn with the company is they should have made their intentions clear on day one. But they tried to play the nice guy even going to the point where Gary Kelly said he couldn't intervene in the seniority integration.
Bottom line though, SWA can and should do what it thinks is fair and right for the business. It's their money they can do what they want.