System freezes when performing intense disk/cpu operations, Disk Utility says the disk is ok Sometimes my system (macbook air, mid-2013, sierra 10.12.3) freezes (beachball + can't really click anything although some mouse movement is possible) and doesn't come back to normal unless I reset it.
This usually occurred during archiving an app, but today happened when I tried opening extensions in safari preferences.

I've tried running Disk Utility, but it says that the disk is ok.
What other diagnostic can I run?
It sounds as though your install is corrupted. You may to boot to your recovery parition (Command-R after the chime), followed by the "Reinstall macOS" option. It should only overwrite the core system files and leave your User/User data/Custom apps untouched, but to be safe you should make a Time Machine backup first.