MacArthur was deliberately trying to undermine Truman, while McCrystal made some statements to a douchebag reporter. Truman did everything he could to diss Truman, from advocating extreme policies, to keeping Truman waiting 2 hours at the airport, not bothering to salute him, and continuing to act poorly after told not to. McCrystal has done one thing for which he will be reprimanded, and then he will hopefully go back to doing his job.
Also, Truman deliberately, and in a sober state of mind, wrote a letter the the Congressional Republicans, criticizing Truman, and with the expectation that it would be read to the whole Congress. McCrystal wrote nothing, was out drinking with his friends and colleagues, and was interviewed with no guarantee that any article would come of it. Again, the reporter was also a douchebag who obviously doesn't like the general.