Not sure I complely understand.
First do you have any 240 loads, or are they all 120 loads. If they are all 120 loads you can use the 208Y/120 transformer and keep it balanced. You just distribute the loads evenly with single pole breakers accross the a, b, c.
The advantage of using 3 wire delta input is effiency and reducing harmonic on the line side. So it may have not been a mistake IMO
