Thats generally the idea, so many times in a series when the villain reaches incredible power, the idea is something is done to either turn the power on them or the heroes take advantage of a situation to suddenly imprision them. Its not a problem if sealing does occur, but generally its much better when there is an actual fight to the point the villian is weakened. Sometimes the solution oddly enough is letting the villian win but then they forgot one tiny detail that leads to their defeat.
In one case, things can go like this with naruto due to the madara situation. Either we can get a good fight we need to finally see madara fall, or things can become piss poor easy and he gets defeated in such an easy and convenient way like Aizen in Bleach. Least with the brothers in the pot or yin kurama recovery situation, naruto and sasuke get the power to stand up and with sasuke fight madara, they did it against obito, it would work again just this time more meaning. Otherwise if that pot is empty, the best thing which is acceptable is either madara is removed temporarily(but later breaks out of the pot by sheer power) while they recover naruto or they weaken him to the point he is able to be sealed away (though this one could occur if they also take the brothers out, heal naruto, then seal him later on after he is weakened.
The problem with Bleach is that it just so happens that he lost to the seal, let alone growing stronger. Naruto gave you the ideas on why it happened before ultimately happens. I don't like how it just is, rather than it just happens. I know they tried to explain but it didn't feel no satisfaction. Hell, at least Naruto carried the theme about friends to the end, having the friends and all others to help Naruto extracting Obito.
That said now I think about it how will this works? Naruto had Minato to expand the extraction to all others but now there's one half Kuruma. So I think Madara defeat will be different. It's like they say, many of these are one trick pony. Hm...