Here is footage of the slide at second base by Leonard Davis which likely ended Daniel Murphy's season. Video quality is on par with that of a surveillance camera, and appears to be pulled from the SNY original teevee program "Daily News Live":
It looks pretty dirty to me, regardless if Murphy wasn't positioned correctly to turn the double play. However, if you were firmly against trying Murph at second base from the get-go, I'm sure you will claim it's a clean play and that his inexperience at the position is the primary reason for the injury. It probably would have been wise to ease him into second base but it's hard to say that this wasn't a dirty slide. Poor Murphy.