Well, that work I don't know how possible is, but it involves mainly AOTC (the same goes for ObiWan knowing about Anakin's marriage, it's a job that has to be done in AOTC to get a better ROTS).

The idea is to tweak the last scene we have of Yoda, Windu and ObiWan to change its meaning, and put in that scene Windu's line "we're keepers of the peace, not soldiers"... so that by the end of AOTC you leave that possibility in the air.

And when you get to ROTS, it's established in the scroll.

"War! (Blah blah blah). Some Jedi Knights have decided to join the war"

And then you put Anakin's line (I'm glad that you chose to serve) in some part of the battle above Coruscant.

I think, that being mainly audio edits, it's easier to do than if it involved FX shots or so.

I think that the main aim of this isn't giving more depth to Windu, but putting Anakin, ObiWan, and Yoda, as characters who distinguish from the rest in their decissions too. If Windu gains depth with this, excellent of course; but the point is to reinforce 4 characters along the movie, or the PT: Anakin, Palpatine, Padmé and ObiWan (and utterly, Yoda)