I propose three possible solutions to the problem:
1) These powerful vassals would not want to join useless Councils at all
2) Advisor posts would be perpetual, even after the Council loses its powers
3) Keep just the five Council positions, but forbid them of joining factions
What do you think?
I think you're putting forth solutions in search of a problem. Taking your suggestions in order:
1) Even without an empowered council, the positions still have prestige. Powerful people will want that prestige.
2) All that does is make it easier for rulers of large realms to keep more of their vassals content, when the idea is to make it more of a challenge.
3) People who hold council positions already can't form or join factions, unless the council is in disarray. (It's also possible that they might be forced to join a faction because of a favor, but I'm not sure about that.
A couple of other points:
First, female vassals can show up as powerful. I'm not sure if they have to be eligible for a council seat in order to be considered powerful (basically all of my gameplay since Conclave came out has been as pagans or Buhddists, and those faiths mostly allow women to be spymasters even without otherwise giving rights to women).
However, minors and incapable rulers don't show up a powerful. Nor do imprisoned rulers. I've pretty much stopped letting any of my direct vassals ever ransom themselves out of my prison unless I have a very specific reason to make an exception, because they're pretty much neutralized as a threat as long as they are prisoners. Often, I'll even move them to house arrest so that they live longer as prisoners. One thing that I think maybe should be changed is that the malus for wanting a seat on the council is greater than the malus for being in prison, so when you do release or ransom vassal, if they're powerful, they'll actually hate you more for letting them out of prison than for keeping them there.
With all that said, I don't worry too much about appointing the most powerful vassals to council seats, except for advisor slots. For the 5 "regular" council positions, I appoint the eligible person with the best relevant stat who is reasonably loyal to me (except for the Marshal position, where I will sometimes appoint a person with lesser skill to stay in my capital training troops or researching tech while the really good generals lead my armies).