From WIKI :
Trial and clan members should be the first to move to even teams. Make a habit of checking the teams each time you’re waiting to respawn. If teams are uneven and you can’t move, ask 3 times in chat nicely. After this check the scores and move whoever would balance the teams best with the !putteam command. Note that there doesn’t always need to be the same number of players on each team for balance – a lot of the time 14 vs 12 can be an even game. Just make sure to check the scores before calling for balance. If you have access to the shuffle command, only use it during warmup (make sure all player have connected) or if teams are incredibly unfair (ex: 11v2) and people are not moving.
If you see someone intentionally join the strongest team, move them to the weaker one straight away and explain to them the rules regarding stacking.
Note: Players are allowed to switch to the team of their liking after a shuffle, provided that the teams are still fair and even. Stacking in any shape or form is not allowed. Admins may use their own judgment on players that do move after a shuffle. If they feel that a player has made teams uneven, they are free to move them back and take action accordingly. Players should respect the admins decision and remain on the team that the admin has moved them to. If a player feels that it's abuse, they are welcome to complain on our forums, NOT on the server.
So IMO if they are not stacking when switching from axis to allies it is OK.