This, for some strange reason, encouraged me to start lre (or 'lua runtime environment'), with the ability to patch issues - both those which are public, and those which are not - without bytecode injection or without limiting the functionality of Lua and ComputerCraft itself, or, writing an entire VM instance which reads and runs bytecode (which also has an insane penalty on performance).
LRE isn't yet ready to replace the BIOS of ComputerCraft, but it can 'interrupt' coroutines and running threads, buffer the ComputerCraft task queue (which also involves extending the length for which things can run before they hit the dreaded 'Too long without yielding' error), and later down the track it will be able to control the flow of HTTP and Rednet activity, as well as other "issues" which can cause server 'lockups' and strange behaviour due to LuaJ quirks - which are features which aren't available typically in Lua 5.1, nor ComputerCraft. As the sandbox now has control over the code being run inside of it without Java-side tinkering, we can make 'user code' conform to whatever rules or bounds we so desire.
The lack of a debug library does make this project quite messy - things have to be juggled back and forth and yielding up and down coroutine 'stacks' occurs. You can wade through my hackery code over at Github. Stuff is pretty documented, but most of the code is passing back-and-forth between coroutines and performing lifting; be warned, strange things ahoy. The code is licensed under the GPL General Public License v2, so feel free to mess around and fork/pull code.
Props to Sorroko for inspiring/prodding me, which produced this