Margin penalty is levied by the exchange not the broker. You can read in detail here.
Zerodha does nudge it’s client’s when margin penalty could be levied. It’s explained in the article here.
About waiver of margin penalty I’m not sure but I’m gonna take a calculated guess and say that it can’t be waived off since the exchange directly levies it.
You can also check this thread for how they are levied.