Filch's crime, for which Harry wants him to serve jail time, is that he sent Draco & co to the Forbidden Forest, potentially exposing them to assault.

Filch testified that he intentionally wanted to expose them to assault and a chance of dying. Quirrel didn't do anything that gave Draco a chance of dying.

Quirrel on the other hand drinks the unicorn blood to safe it's own life. As far as Harry thinks Qurirrel also only stunned the centaur and wanted to safe Harry's life.

For Harry morality being alive and saving lifes is very important. Short term pain and being stunned doesn't factor much into Harry's utility calculations.