Personally I think it was a mistake to make a blanket allowance of the MM races in the first place, since the intro to that section makes it clear that they may not be balanced:
In general, these traits and powers are provided to help Dungeon Masters create nonplayer characters (NPCs). This information can also be used as guidelines for creating player character (PC) versions of these creatures, within reason. Note that these traits and powers are more in line with monster powers than with player character powers.
I would have considered them for inclusion after the game was running for 3 months, just like for new content.
But that cat's out of the bag now, so I'd suggest we officially add two subraces of minotaur to the setting (perhaps the "Angus" and "Longhorn" Minotaur). The Angus, having no horns, would get Oversized Weapons and the MM stats, while the Longhorn would get the Dragon stats and access to the feats. (We could even decide on a feat-by-feat basis which are appriate to give to the Angus, bearing in mind that its basic ability is more powerful than the Longhorn's.)
Also, I'd say the Minotaur with oversized weapons is problematic not because it's better than the Dwarf at all points, but because it's perfect for min-maxing a fighter. Str and Con bonuses AND oversized weapons is too much. The Dwarf has powers that are better for a fighter alone than oversized weapons, but the Wis bonus doesn't help quite as much. When you're in a persistent world where strangers are playing together they're going to be more sensitive to having one race that can't be touched for damage output.
Maybe a good fix would be to give the L4E minotaur all the powers from the MM and Dragon article, and add a penalty for the use of oversized weapons that brings it back into balance. For instance they could be prohibitively expensive, or have a critical fumble chance. Anyone who feels that their character is being nerfed would be compensated by the fact that they'd pick up extra abilities in exchange for some penalties, rather than having to give up their ability.
I'd also like to suggest that if a class or race gets altered, characters of that race be allowed extra retraining the next time they level up so they can swap in some of the new feats and powers easily.