You need to do a DosDevIOCtl with Category 4, Function 56. Use a 0xFFFF for the Hot Key ID. Set the other values to 0. This will toggle <Ctrl><Alt><Del> and <Ctrl><Esc> and <Alt><Esc> on then off on the next call. Note that this does a little more than what you want since it also disables <Ctrl><Esc> and <Alt><Esc> so you may run into problems getting around your different sessions when you've got it disabled. Other than this there is NO WAY to disable <Ctrl><Alt><Del> under OS/2 and believe me, people have tried!
Credit: Mike Brown