Song could still be placed on the 60-day DL and not pitch at all this year; that would just make him subject to the full Rule 5 requirements for all of next season (i.e. on the major league roster all year, or for 90 days and otherwise injured).
The question is can they actually legitimately do it (based on both his actual physical status and the potential for a grievance), but also, would they even want to? He still wouldn't be easy to hide on a team with continued World Series aspirations next year, any more than Marte (or right now, Hoffman) can keep their jobs for very long.
They may legitimately be taking great care with him given his long layoff from the game, and can also make that argument to MLB if necessary. Or, he is quietly throwing a lot more than we might think.
It is bound to come to a head pretty soon: to even get his 90 days he would have to start his 30 days of minor league rehab by June 1 or so. And if they were able to get MLB to allow some sort of waiver (there was talk of a 14-day) to get him more time in the minors it would have to be even sooner. Don't see how the "two 45-day periods" would even work at this point.
He could still also be traded. Would have to be somewhat sooner than the deadline (well, to anyone other than the Red Sox but they wouldn't be offering the same value as other teams).