What will happen if Streak strategy exit condition is not met for the day?

Suppose exit condition for MIS order is not met will I be charged 50 rs extra for Zerodha to square off or should I manually exit it to avoid that charge?

You should manually square-off your open position before 3:20 PM, after this, it will be squared-off by RMS, for which charges of Rs. 50 + GST will be applicable. Streak has also explained this here.