If its embedded in the video then you cant, otherwise you may be able to de-mux the video and audio separately and re-mux them back together (in mp4 or whatever you like) but youd probably have to use mp4box and mkv extract in command line.
I can keep the .mkv-container. Thing is, when I try in mkvmerge, I unselect the subtitle track and push "start muxing" I get the message "mkvmerge FAILED with a return code of -1." in the status and progress line.