According to the Daily News Jose Reyes has a completely torn hamstring behind his right knee,
The article goes on to say surgery should be able to alleviate the discomfort and allow Reyes to return unimpeded next season. Surgery is not necessarily as ominous as it might sound. That tendon is expendable, and is sometimes partly removed and inserted into the elbow when a pitcher undergoes Tommy John surgery.
Ugh, just get it over with it. Speedy recovery Jose.

It seems like this may have been what they were trying to avoid all season and at least get him back for the end of the season, and just do the offseason surgery afterward. The medical staff tried a number of rehab techniques that I had read about including a newer experimental therapy involving blood plasma. Apparently this worked well for Hines Ward and Takashi Saito, but not one single Met.
http://www.nj.com/sports/index.ssf/2009/07/cuttingedge_plateletrich_plasm.html