If you run it on a dedicated and you have a gamelogic named Server, then that script should run only on the server.
Since many missions already use the gamelogic named "server" what you may want to do is have whatever your init file is check to see if "Server" is defined or not, and if not, then create the gamelogic locally with:
?!Local Player : createVehicle "Logic"
Now, if the server is hosted, then it gets trickier, because the local server also has a local player.
BTW when I tried the test mission with the Strykers on the island and the ship with the cruise missiles, if I got in the Stryker and started the radar, then stayed in the vehicle until the cruise missile hit me, I would die, and seconds later ArmA would crash. I wonder if there's not some exception in a loop for the death of the player while the radar is running or something. Anyway, thought I'd mention that.
I read the instructions for adding the missiles, but couldn't find the exact scenario I wanted. In RTS-IV, when someone builds a Vulcan/Shilka, I'd like that vehicle to have the ability to fire missiles. So I copied over the mando_missiles folder. Do the vehicles then need to exec a specific script in order to have the missile work? I don't want to use the menu interface or anything. I just want the blasted Vulcans and Shilkas to be able to actually shoot down aircraft. From what I understand, your scripts add some automation to that, right? Or am I misinformed?