Eric,
Why not upgrade your hosted system to php version 5.6? Maybe (a big maybe) your Moodle will work.
Since there are probably thousands of products that could be run on a hosted server, do you really think that cPanel and/or the upgrader product should know about the latest requirements of all? Consider turning off auto upgrades on cPanel. In the server world, a lot of responsibility is put on the system administrator -- I think this might be you. (I might be one of you too, a professor and part-time moodle administrator. )
Well, you can put this issue into tracker but it really won't help. Moodle actually does check versions of php, and usually warns you. But your system administrator can override this warning, which is what your auto-system-administrator probably did.
As another suggestion for your future, consider learning how to install and upgrade moodle on your own. It is really not that hard, and it will probably pay you dividends in the long run.
(Incidentally, I use cPanel myself. I use it to upgrade my versions of php. It is really pretty easy. But I don't run any other products on my VPS. Be careful, upgrading php might break some of your other applications.)
If you have some good backups of 3.1, you can try reinstalling moodle 3.1. This might be a good time to learn about backup and restoring your moodle (hmmm, more to learn. )
(Image below borrowed from Mary).
