This is absolutely possible.
Go to NCrunch->Set Engine Mode->Customise Engine Modes
Then choose the engine mode you want to ignore categories in.
On the bottom pane, under 'Settings to be overidden by this engine mode', go to Filters->Tests to execute automatically.
Click the pencil.
Click add condition.
Use 'does not have category', and enter the name of your category. Save all changes.
When this engine mode is active, the engine will not automatically execute tests marked with the specified category.