His contract is up after 2015, and they haven't extended him yet.
Which is still two seasons away.
Internal strife or not, the miners were a doormat for the decade of the 2000s then Harbaugh shows up and takes a 5-11 team to the NFCCG the next year, develops the roster and creates a perennial contender. They would have been retarded to ship him out, and it would have ended up costing the higher ups who shipped him off their jobs in a year or two.