Tangent: To deny those bare-metal instructions with static analysis, you might also have to flat out deny certain sequences of instructions that, when jumped to "unaligned" would also form the forbidden instruction. That might break innocent programs, no?
Simple: don't allow unaligned jumps. Google's NaCl already figured out how to do that ages ago. (Eg you could only allow jumps after a bit-masking operation. Details depends on architecture.)
But yes, unless you solve the halting problem, anything that bans all bad programs will also have false positives. It's the same with type systems in programming languages.
