The cost should be considered. So should the precedent. And so should the reasons that a man like Belichick might pay that cost.
The Patriots have several more years to play for championships, as long as Tom Brady is still Tom Brady we will be in the mix. And it's entirely possible that we stick the replacement and are still competitive after he goes, if Bill does a good job coaching the younger replacements.
Now let's factor that into the decision. The Superbowl is important, but is it possible that another consideration is even more important?
Let's consider the things that Bill Belichick does to create greatness in this franchise. I think that it's a pretty fair thing to say, that bill knows what he's doing more or less. Now obviously, if he still makes the decision to put the Superbowl win at risk by benching Butler, he's protecting something more important to him than Superbowls.
Since there isn't very much more important to a football head coach than Superbowls, I think we can narrow the reasoning down to 1 of 2 things -- either Bill was on an ego trip, or he feared an existential threat to the Patriot Way if he let Butler carry on as if nothing was wrong.
Since Bill on an ego trip would be INCREDIBLY out of character, I think we've successfully narrowed down the core of the issue. The exact allegations of Butler's behavior are almost meaningless in that context. Whatever the meat of the problem with Butler was, the bones of the problem were that he represented a precedence-forming threat to the team culture that Bill was simply not prepared to tolerate.
The Patriot way is one of the few things in all of football that has a legit claim to being more important than any one Superbowl. The strong team culture that Bill has built up has had a huge role in producing at least 3 of our 5 Superbowls. Watching that team-culture edifice crumble in the name of short term gain is not a price Belichick would ever be willing to pay -- not unless he was short timing it and knew he was done at the end of the year anyway, which thank goodness, he doesn't seem to be acting as if that's the case.
Whether you like it or you don't, I think that's the core of the issue here. Allowing short-timing guys to ignore the rules and do whatever they want, whatever "whatever they want" happened to actually be in Butler's case, is not a path Bill will go down, because the end of that path is the death of the unique culture he's built in New England, and if he makes an overt decision to let that culture slip, even to win a Superbowl, he'll never get it back again. Pro athletes know a loophole when they see it and it's very, very hard to reestablish discipline in a team once you start to let things go.
If Bill honestly felt that tolerating Butler's sabotage of the Patriot way, whatever it happened to be, would have opened the entire Pandora's box of player disobedience and disregard for the rules that's sabotaged so many good to great teams (most notable recent example; the Steelers), then he had to take a stand against that. Even if it cost a Superbowl.