"Use MkvToolNix. The mkvmerge tool can do exactly what you want. It's a very capable Matroska manipulator and should be able to remove any kind of stream from an MKV without recoding all the other streams.
On Windows, download the latest version from here. Just run the installer. On Linux, you can find the package mkvtoolnix in your repository, or alternatively download them from the homepage. On OS X, the easiest way would be to install mkvtoolnix through Homebrew.
I think one of these commands will do what you want: # assume input.mkv has 3 subtitle tracks # remove subtitle track 2 (copy 1&3) from input.mkv & save to output.mkv mkvmerge -o output.mkv --subtitle-tracks 1,3 input.mkv