Someone explained a situation where she had arrived as one of the first to defend the towers of a guild in their alliance. As more people gathered, she was warped away by the new CC system.
This needs a revision.
The people already there, should be able to stay in the zone untill they die (maybe have a delta of 2 - 4 when area has reached max cap, just to make sure people are not holding other people out on purpose). The way it should work (imo) is that the last to come has the fewest rights - compared to the ones that arrived early. The important thing is to balance the cap so it reduces lag, and still is fair and good fun.
And of course, you will hopefully revise where you have placed your warp stations (where ppl warp to when displaced by the CC system). Having people warped into nowhere is basis for frustration and deflating the fun of NW. IMO the warp stations should be placed NEAR to the pvp action, but on the other side of the zone border. That way, people who have been warped away can que up outside the pvp area, waiting for someone to die, and fill their place RAPIDLY. This would also mean having to use tactics when assigning people to enter the area, as you would want key personel to be able to get back in.
Alternately making tower controlled areas their own SMALL zones (or protected by invis walls, as mentioned by Cz), making servers concentrate on those areas in particular. (I.E. Broken Shores and outside of TIR are example of areas not good for crowds, as the servers have to focus on a larger area.
I know you didnt ask for suggestions, but thats what I give you. Sorry