I don't think this is just a Confederate team problem or a matter of tweaking the team morale to get the desired balance. I really feel like individual fights should have more transparent dynamics than what we have. The players should feel the success of driving the enemy back or bleeding them out. That just isn't happening now.
The basic concept right now is about forcing players to fight in close formations and even standing over crouching. If they don't, they hurt the team. I'm not saying that's a bad thing to try and force players to do that but making the entire win / loss calculation about that just doesn't result in what feels like a natural conclusion to the round. It isn't the best way to accomplish that.
Each round should revolve around capturing a location or a series of locations. There should be varying levels of winning/losing and even a 'stalemate' conclusion. Teams should literally have a solid number of reinforcements they can put in the field like there was before - it doesn't have to be shown to anyone either. So there's that dynamic - every enemy whose killed is one less to deal with. A team can be bled out by hard numbers of losses or it can affect their victory and turn it into a "pyrrhic victory."
The effort to keep players in close formations (and even standing) should be refocused to solely effect when and how the individual player can spawn. A formation should be judged by its strength and integrity and the second you are killed in that formation you are judged based on that. If it had twenty guys, better than ten. If it was 40 guys but split in the middle then maybe consider the half the player was killed in only. Based on that you are either allowed to spawn behind the line (flag bearer spawn system) in short order (with a minimum of 10-15 seconds and a queue to wait in) for an excellent formation possessing a flag bearer or at the rear with the gear after a longer time (with a maximum of two-minutes) for being isolated 'out of line.' You can be creative with these. IMO a flag bearer should not be essential to spawning on a line. A five person line should yield a much longer spawn time than a 20-40 person one. Players can select where they spawn but options are limited depending on the quality of your death. The wild contrast between the results of your spawn will encourage players to 'behave' and will also give these players more time on the field while making.
I really feel like it adds a bad flavor to punish the team for the actions of the individual. It also results in last second round decisions that don't always make sense. Spawning at the line is an enormous advantage that should be used. Maybe even make it so the very best line can spawn people already loaded.