How to prevent IntelliJ IDEA from deleting unused packages?

Disable File | Settings | Editor | General | Auto Import | Optimize imports on the fly.

Normally you don't need to add imports manually, IDEA does it for you.

For Scala developers: you can have enabled

Settings > Editor > General > Auto Import > Optimize imports on the fly

but add exclusions into

Settings > Editor > Code Style > Scala > Imports always marked as used: