No, sorry.
When you join as commander, the server will decide on which team to place you with. But if you join as normal soldier and dont what to command the team you ended up with, just switch teams, press Esc, press "Team Setup", press "Commander" in the top bar next to the "Squads" section and press "Take Command". After that agree that you will become a commander and lose your soldier slot and you will be commanding that team.
Note: After you do this, you cant switch teams no more and will have to disconnect from the server and connect again to command the other team. Or you will have to wait till the match ends and server switches you to the other team.
