There are a couple of solutions here.
I don’t think there is a way to stop the Quick Controls from being enabled by default or a way to stop the QCs from being automatically “retrieved” from the instrument and assigned in the inspector. BUT, you can go to devices -> device setup… select Quick Controls", and in the drop down box, where it says “MIDI Input” select “Not Connected”. What this will do is tell Cubase that nothing is to actually control the Cubase Quick Controls. You will still be able to use your controller to control parameters with the “Learn CC” function, etc. You can also still control the “Quick Controls” in a VST Instrument like HALion Sonic SE with your controller with the MIDI Learn assignment (don’t confuse Cubase Quick Controls with Instrument Quick Controls). In this method, the Cubase Quick Controls are still assigned to the instrument but NOTHING will make them move.
Another solution is to make a habit, when creating a new track, of either disabling the Quick Controls in the inspector or clearing them out (both one button operations, which, from your post, you already seem to be aware of).
What controller are you using? I ask because Quick Controls are very convenient and powerful if you can set them up in a “spare” bank on your controller (if it has the capability).