This has not been some long-running conspiracy - Myself and some other representatives spent time today discussing with Lontahv and Hoikas what sorts of changes could be made to work on improving the Guild's position within the overall MOULagain community, and how we can make sure we're able to work with Cyan in the future, as fan content and open source progress.
The decision to remove the note was one Hoikas felt he and Lontahv could make without a public vote, since the council has the power to manage "Day-to-day guild operations, like forum layout, adding new features to the website or guild infrastructure".
As far as the PMs you sent, Hoikas' view is that if it was a major issue to you, then you should have brought it up for a vote by the representatives. It's the position of the Council that the banner falls under "forum layout". I'm inclined to side with him on that point, though I think a response to your PM explaining the clause he was working under would have been preferable to ignoring you.
I think both you and Hoikas agree that things should be done within the guild structure, there's just a bit of disagreement over just what that structure means. If you feel the "non-criticical matters" rule is being applied too broadly, I would urge you to bring it up for debate in the proper forum.
Obviously some of this would be preferable coming directly from Hoikas - I'm posting it on his behalf because he's liable to be a dick about these things.
<Hoikas> I do hope that someone will make a prettified version of my post for me XD