You won't hurt the gate if you give it the appropriate voltage, the transformer will set that according to the turns ratio. You just need to make sure your transformer can tolerate the Volts x Seconds product. I'm used to MOSFETs, but an IGBT gate should be similar, use a 1:1 transformer and drive it with 12V, the gate can tolerate more than 20V, probably 30V.
Multiply the 12V by your longest pulse width and ensure the transformer is designed to that much plus at least 20%-30% margin.
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