There's a simple way to quickly figure out which of our components' files are safe: go to Components, Akeeba Backup (and Admin Tools etc) and open the component. Wait for 10 seconds. If no Big Red Scary Message appears telling you that your installation is tampered with you can safely assume that the component's files are safe. So just go to the PHP File Scanner and mark them as safe (click on the red icon in the second to right column next to that file). This will reduce the number of files to about half :)
As for the rest of the files I suggest that you follow our documentation instructions. I know that it's a tedious job but you only need to do it once. Afterwards you can just run a scan after updating Joomla! and/or its extensions and mark all new and modified files as safe. This way any changed / unsafe files in intermediate scans are guaranteed to be actual issues (hacked files) instead of false positives.
Nicholas K. Dionysopoulos
Lead Developer and Director
🇬🇷Greek: native 🇬🇧English: excellent 🇫🇷French: basic • 🕐 My time zone is Europe / Athens
Please keep in mind my timezone and cultural differences when reading my replies. Thank you!