Why Rocco?
Only FFC or Puzo or a very few others could really speak with authority.
The obvious allusion is to the murder of Lee Harvey Oswald. It may not be any deeper than that.
If it were any deeper than that my guess would be that Michael wasn't convinced that Rocco still wasn't somehow involved with Roth (after all he was in charge of security) and wanted to test/punish Rocco by making him handle the job personally.
It doesn't seem to make sense as most people know that Rocco was at the very least linked to Michael but maybe the viewer was supposed to think that at this point Michael's influence is so strong that he can get the media or authorities to ignore such things.
But this of course is ALL wild speculation.

I really don't think it goes much further than the homage to the LHO murder.