While I have no inside knowledge, I'm 100% sure that that's the reason.
I guess it worked too which is unfortunate since it helps reinforce that movies need to be PG-13 to make money and fortunate in that it did get the movie seen by more people. In the end though, the movie will be seen by more people on video so the extended/original version is what most people will end up seeing.
Except if you Netflix the DVD (not the Blu) as I did, where the only option was the theatrical cut with no extras. A "Rental Exclusive" edition, hooray. I enjoyed it enough to consider picking up the Blu eventually.