Rather than "deleting" a team registration, the correct way to remove a team from a League is by switching their Team Status to "Cancelled". This will remove the team from the default "Teams and Players" list for a League (Note 1: if there are any "Cancelled" teams in a League, a header called "Cancelled Teams" will appear under the normal list of teams, you'll still be able to find their info).
When a Team has a Team Balance and you switch them over to "Cancelled", a popup will appear and ask if you want to change the Team Balance - you will want to set it this to zero. If the team gets re-Confirmed, the Fee will be applied again. Players and Captains will not automatically be refunded when you cancel a team. If you wish to refund the players, do so manually before cancelling the team and zeroing out the balance.
Note 2: Cancelled teams will remain on the schedule for any games that have already been scheduled.