What options are open to the CIC and SecDef in these situations?
Traditionally, the President doesn't interfere with the process, but may issue a pardon (as in the Calley case) after the convening authority has reached a verdict. (That is, of course, if charges aren't dismissed by Gen Mattis after each Article 32).
The Sec Def may manuever behind the scenes, and express the President's will, but has no constitutional authority.
Regarding the NCIS, no one has ever shown any inclination to reform the agency. There was an opportunity after the USS Iowa turret fiasco, but the only change seems to have been a name change: from NIS to NCIS.