If you ask me, simply making the melee system more eloquent would fix a lot of these issues. Once you're able to more reliably aim where you stab on a person's body and manage to land a hit on the center chest, neck or head and that being a 1 hit kill it would solve the problem. Yes the officer would still have an advantage in CQC but not something two or three men with bayonets can't handle. On the flip side those men armed with muskets have a huge advantage over range. So that counts as balanced in my book.

I reckon that at some point you would also be able to fend off from melee attacks if you're armed with a rifle yourself. Simply make someone armed with a pistol incapable of doing this (e.g. keep that the way it is now).