I noticed a post this morning where Lieutenant General Sands agreed to play with any rules except rifle effects. That coincides with an ongoing discussion between Marechal Garry Cope and myslef. So General Sands and Marechal Cope please forgive me for taking your names in vain, but I want to defend this rule.
First, let me say my defense is limited. My own studies indicate that rifle effects should be in effect only for 1776 and the Texas Revolution battles in MAW. In MAW and 1812, and in what I have read (though little) of FIW, tactics were more along European lines of simple massed fire. But in the two revolutions there was a clear and consistent practice of firing at officers -- so it would seem the rule is valid from a historical standpoint for those wars.
I also want to add that the rule should only be used for real rifle units. Although there is reason to believe that, at least in early battles, the Americans aimed for British officers with their muskets, as well, it is unlikely they did significant damage in that regard. A good example of this is Bunker Hill, where the British, in spite of a terrifying fire, maintained more than enough officers to continue reforming and leading their units into battle.
There are a number of scenarios in 1776 where the militia is armed with rifles. Most (perhaps all) of these should never be used. Militia was virtually always armed with muskets. I would say always but then some wise guy would find one time when they were armed with rilfes.

Anyway, most of these scenarios have variants where the militia are armed with muskets without bayonets. These are the scenarios that should be used. In some cases this will, in itself, negate the rifle effects, and in those cases that's how it should be, because that was historical.
All that having been said, there is a strong case for using rifle rules with legitimate rifle units. In terms of history, it just makes sense. But, though I detest play balance rules, I think there is also a good case for the rule in that regard. The British have one overwhelming tactic that the Americans can't match -- melee. The only real American defense against that tactic is to stop the British from reaching their lines. If you take away legitimate rifle abilities, you make that even harder than it already is. The effect is to make the British melee proof and almost make them invincible. This twists historical tactics.
A good example of this is the Saratoga battles, won largely by the very type of rifle effects we are discussing. While I am not an experienced enough player to wager victory by the British every time without rifles, I am a good enough historian to know the outcome of those hard-fought battles would have been materially changed.
In all fairness, if the British/Mexican player asks for the rifle effect rule to be deleted, he should promise not to initiate any melee combat during the game. That sounds illogical, of course, becuase it takes away the best weapon of the British. But IMHO it does the same thing to the Americans/Texas when you strip them of legitimate rifle effects.
Just my thoughts on the matter.