But Binance founder doesn't work for Binance anymore so why pardoning founder help Binance?

The current head of binance (and cofounder) is Yi He. Who happens to be in a relationship with CZ and is the mother of his children.

Because it sets a precedent

According to Binance, he owns 90%. Whether he is CEO or not probably doesn't prevent him from influencing Binance operations to support Trump's coin.