Bruno,
I have a 5000 series scope at my desk - hopefully at least one of these ideas might help on a 3000.
I was able to disarm the scope by...
1. sending a reset command or running "Reset" VI (though it was destructive to my current settings)
2. running the "Force Trigger" VI
3. running the "Set Acquisition StopAfter Mode" VI with "stop after mode" enumeration set to "RunStop" (same as pressing button)
I didn't try this but you can also programmatically set the trigger mode from "Norm" to "Auto" to get the scope in a more communicative (less armed) state.
Good luck!
Bart C
National Instruments
Bart
LabVIEW R&D