There is no easy way to do it, it seems.
So I wanted to say that I couldn't afford to do an upgrade on my server and my service provider wanted $30 for IPMI access. I have searched countless forums on how in the world to fix this problem. I set Passthrough on and all my datastores vanished and said I need to add a datastore. I couldn't remove Passthrough because since the file system is mounted in read only for some reason you can't ssh in to the server and edit esxi.conf to fix the problem. This is my first tutorial on how to do this, so don't bash my head that it's sloppy.
1. Boot with a debian or ubuntu live cd
List your drives / partitioned: Open a terminal window
2. type parted -l
Mine was sda5
3. mount /dev/sda5 /mnt
4. ls /mnt/
5. cp /mnt/state.tgz ~/
6. cd ~
7. tar xvf state.tgz
8. tar xvf local.tgz
So you get a etc folder now. Go to /etc/vmware
9. nano esxi.conf
10. Replace everything that says passthru with vmkernel
11. Save the file
Now lets copy the file back to the mount point, but first we have to recreate the archive.
12. tar czf local.tgz etc/
13. tar czf state.tgz local.tgz
14. cp state.tgz /mnt/
Done. Reboot and everything should work as it did originally.
This was tested in ESXi 6.0 and 5.5.
Hope this will help others that are trapped in a similar situation. Of course you can reinstall but a lot of people wanted to know how to do it. This which is basically 14 steps can probably be shortened. I hope that my first contribution on this forum is not overlooked.