Unless I missed it (I admit I skimmed towards the end) The author does not discuss at all the actual remediation that was taken. I would love to hear more about that.
1.1.104: https://github.com/Rseding91/Factorio-Lua/commit/4d924b69808...
and
1.1.107: https://github.com/Rseding91/Factorio-Lua/commit/ce12474c7fc...
The most relevant part was the change to luaB_load in 1.1.104 which simply disabled bytecode loading.