I agree, the film was far better than I expected... I did expect a lot more cheap shotting and I have no doubt many scenes were filmed but were recognized to simply not be funny or to be too predictable and were left on the cutting room floor.
The movie itself was a pretty fair homage to the source material, and far better than I had expected.
Alsi, the nuns were portrayed as good, caring, and decent people. They are exasperated after dealing with the knuckleheads for 25 years, but they clearly love them, even going out of their way to spare their feelings.
The Stooges themselves go out to save their orphanage, motivated by loyalty and live.
The boys themselves are bound by fraternal love.
Anyone finding something to be deeply offended about is just looking too hard.