Nearly all serious compilers have at least one representation which is not isomorphic for all programs. (It is homomorphic, which is required for the compiler to be correct.) As a consequence, at least some programs will be mangled beyond recognition.
Just because it's hard doesn't mean it isn't worthwhile to do, or that everything the compiler does must be reserved and shown in the IDE. I'm also not suggesting that this compiler feedback is the only IDE improvement we make. I'm observing that the entire way we develop software hasn't fundamentally changed in decades, yet every other aspect of computing has. Even something that roughly seems the same like word processing is now collaborative and in the cloud with real-time updates and social threads.
Light table is one IDE that is trying to question some assumptions -- like that files are important and that everything must be 1 line spaces apart in mono font. This is the kind of progress I'd like to see.
It does seem reasonable that there be a way, even if difficult, to highlight a bounds check that gets optimized away. If we start from the problem we're trying to solve (show eliminated code that poses security risks... such as bounds checks or erasing memory) rather than the general problem (reverse all compiler changes), then things become more tractable.