I think that line about Rocco building a secret regime was careless writing. Rocco was Clemenza's man, not Michael's. And it would be difficult for Rocco to build a secret regime under Clemenza's nose without Clem knowing about it. Since at that time Michael didn't know who would betray him, it would be a signal to Clem that he didn't trust him.
Ntra la porta tua lu sangu � sparsu, E nun me mporta si ce muoru accisu... E s'iddu muoru e vaju mparadisu Si nun ce truovo a ttia, mancu ce trasu.