The MKV container supports forced tracks, though the problem is not all players support this feature. XBMC does so you can have subtitles globally disabled but the forced subtitles will still display, couldn't say for other players (MPC-HC doesn't).
* Download MKVtoolnix and use MKVmerge
* Drag and drop the file generated from MakeMKV into it
* Either select an existing subtitle track or drag and drop your SRT file into it.
* Set both "forced track flag" and "default track flag" to yes
Click start muxing to generate a new MKV file and hopefully your player supports it.