It's by a good deal, as Mr. Buu is pure good, and Majin Buu still had his evil side inside of him; Mr. Buu was pretty much what was created when Bee died and Majin Buu expelled his gray evil side, he had a significant power reduction
I know that Evil Buu was stronger than Mr. Buu, however, during their fight, it seemed as though Evil Buu only had a slight advantage over Mr. Buu. He certainly wasn't picking him apart.
However, by your reasoning, you're basically saying that Majin Buu and Super Buu were equal in power. Majin Buu was basically Mr. Buu with Evil Buu absorbed and Super Buu was just Evil Buu with Mr. Buu absorbed. Unless, of course, you're saying that evil is more powerful than good in the DBZ Universe.