The most logical solution is to include the shifts in the roll but to grant greater latitude to wizard in determining the taken out result for damage done by control shifts as opposed to weapons ratings.
While I am sympathetic to the viewpoint that high powered weapons rating should be limited before they become lethal, it does not make sense to punish a character for doing a good job controlling their evocation. Such a situation strikes me as creating a gotcha situation designed to deal with the fact that some GMs do not like wizard PCs principal combat power throwing a punch that puts it on par with the combined speed, strength, etc. powers other PCs get.
In designing the rules for the game I am GMing, I keep running into the same problem developing one of these house rules: If one of my PCs brings a low yield attack but has high discipline and gets lucky, why should they be punished for exercising excessive ccontrol over their power? The whole point of control is that it well controls the use of power. Otherwise, it is impossible for a player to effectively play a spell caster if they cannot calculate a low yield attack setting because they may roll too well (or the opponent rolls badly)
The argument is made that such screwing of evocators is necessary to maintain story cohesion, but it leads to the result that Harry Dresden is better able to safely incapacitate an opponent than would Elaine Mallory who, by the rules, gives up a an extra mild consequence, and suffers a reduction in her spell casting power, specifically to have the ability to exercise absolute control over her spells. This makes no sense and justifies a simple rule that, below a certain weapon rating (I would say 2-3), the rules in the book should be followed with regards to taking out an opponent even if one of these house rules is imposed.