What Montessori is your son at? My son is at Sunny Hollow in St. Paul and has been there for two years (he is 5 now). Last year, during his first year in the children's house, he went through a period where he "hated" school and I also seriously questioned whether it was a good fit for him, especially because he is very social. We stuck with it, however, and that was a very good choice for us.
I do think lots of kids have a hard time adjusting to the free choice and self-direction, especially if they generally prefer to work in groups or get adult approval (as my son does). What I realized, however, was that Montessori was a great way for my son to build skills in areas that were not natural strengths. Because I felt really confident in the school and the program (his teachers are wonderful) I decided that it was worth it to push through the "boring" and "work" of it all so that he could develop some independent work habits and self-discipline.
Now he is in his second year and absolutely loves it (and has for awhile - he was only unhappy off and on for about a month last year). He has learned a lot more than he would have in most play-based programs, has tons of friends and a real interest in learning.
I would definitely give it more than two weeks and I would talk to the teachers about giving him the most "fun" work possible to get him interested in the idea of independently choosing work.
Good luck!
B.