One more solution I could think of. Zerodha should separately keep extra margin when we take the position itself. So margin utlised may go negative in our account as per zerodha but it will actually still be positive as per exchange.
Example: Lets say 1lakh margin is required to take a position. Let Zerodha block additional 10 percent as safety margin. So 1,10,000 would be required. Now when available cash goes negative there would be Nudge for balance going negative. But short penalty wont be imposed since as per exchange it is still positive. I have given an example of 10 percent, but may be 5 percent would also give us enough time to change our positions.