The problem goes beyond translating 16-bit instructions with 64-bit instructions. There is also the ABI (Application Binary Interface) used by the program to communicate with the rest of the system. A 16-bit program likely uses a lot of DOS calls and it's not unlikely it tries to access hardware directly too. There is no way this can be translated automatically. Even if such a solution existed, I highly doubt the result would be more efficient than running in a virtual machine (which actually is very efficient). Further more, programs written for 16-bit environment are often not very scalable, and completely unable to handle amounts of data beyond the capacities of the original target platform.
So I'd say there are really just two realistic solutions: Run it in a virtual machine. Or if that doesn't cut it, write a new application from scratch that does the same thing.