I assume the OP is talking about the required chair's letter for a lot of/most IM programs, not just getting a normal letter from your dept chair.
To the OP: For the programs you're positive don't want a chair's letter, I don't see any reason to include it. They basically say the same thing your MSPE says anyway, so if your chair didn't include any personal touches it shouldn't really matter. From what you wrote, I assume the chair barely knows you, so can't really speak personally to your qualifications? If not, then his "big name" won't matter, because the program will know he only wrote the letter because he had to.
If my assumptions are wrong, please feel free to ignore/chastise