It's not like FOX said "OK, we demand this and this and this." It's been made pretty clear they were never very unfair, and I'm pretty sure JOSS decided to give them those episodes. Had he refused to do five stand alone episodes do you really think FOX would have put up a fight? No. At the very most it was just a compromise that they both agreed on.
That being said, I thought despite the fact that the episodes were supposedly "stand-alones" they all did an excellent job of slowly building towards episode six and I wouldn't get rid of any of em, they were all enjoyable.