Assuming the simple case of 2 wow clients and straight repeating:

If wow #1 has forward as ctrl+up
and wow#2 has forward as ctrl+alt+up

If you press ctrl+alt+up to move #2, then #1 will move beacuse ctrl+up are being pressed, if there is nothing else bound to ctrl+alt+up.

You can stop wow#1 from moving by binding ctrl+alt+up to an unused action button, or to a null macro.

There is no way to specify strict keybinding parsing only. (like the [nomod:alt] grammer in a macro could do)