Ye Gods! While understanding the inner workings of IL is valuable, modifying it on the fly can only be a recipe for pain. If you really need to use the C# code injection feature I’d switch to the DLR and IronRuby or IronPython.
The GAC’s strong name support is in fact designed to stop this very kind of tom-foolery so I can imagine that you would (quite rightly) run into security impediments pretty quickly too.
Having said that; it’s not a powerful/dangerous as softICE and I never go into too much trouble with that… 🙂