If you don't want to mess with the registry, you can use AutoHotkey along with #IfWinActive statements to define actions for different programs (for example, you can have multiple definitions for the same hotkey, but they will only fire for the given #IfWinActive program). You would keep your original statement but apply an empty #IfWinActive to capture/ignore keystrokes when made to any undefined program, and then add secondary #IfWinActive / hotkey definitions for additional programs/actions where you actually want to use that key combo to do something.
A second approach would be to rewrite your hotkey definition to send some other little-used hotkey combo via SendInput or similar Send command, and then trigger off of the redefined keys if you need to. This is less efficient but may be easier to understand (or not).
For example, you could send Ctrl+Alt+Shift+F12, which most programs probably don't use. If you wanted to recapture the hotkey however for certain programs, you might also need to pay attention to the SendLevel.
In general I would recommend the first method above and just define that key combo to do whatever you actually want it to do for the programs you care about, and ignore all the rest with a duplicate / generic hotkey such as the one in your original post, but with an #IfWinActive statement in front of it.