Qualified immunity concerns civil liability. Prosecution is about criminal liability.

Civil liability is helpful because tax payers do care about $$$ (if judgements/settlements are starting to eat major part of budget the people will start to care on how to lower those costs) and victims are not limited by what prosecutors are ready to do. The QI is especially problematic because it has essentially become "did someone prosecute cops about this before" because that's effectively the only way to establish precedence that allows you to get across the QI-line in future for sufficiently similar conduct. And like you said, prosecutors are often unwilling to prosecute cops.