I think the first thing to do is to break down your premise that they are doing it "for no reason."
You are correct that clicking the pen does not engage the pen in its role as a writing implement. But if so many people are doing it (this writer included) it must serve some purpose to them.
The Wikipedia article you link to includes a list of causes of what it describes as "habitual pen-clicking" (sic), ranging from boredom and idle thinking to harassement to autistic self-stimulation.
Looking at these causes, I would suggest that the two best strategies to avoid pen clicking is: 1) remove the feedback from the clicking mechanism, and 2) where possible provide a more tempting (but less annoying feature).
- The clicking sound, while the most annoying part for other parties, is only part of the feedback mechanism when retracting your pen. There's the sensation of pushing in the button, and a small physical kick that is felt in the pen button and throughout the pen when the retracting spring is called into action. I'm not an engineer, but supposing you couldn't suppress the sound I would focus on somehow suppressing the sensations.
This, however, comes at a cost. The feedback also serves a benign purpose of telling the user his action has taken hold without actually looking at the pen to see if the ball point is in or out.
- To enable a user to displace his need for fidgeting, you could offer a silent little mechanism. Imagine, for instance, a ring around the top of the pen (just below the "clicker") that you can slide around silently without any other repercussion.
Anecdotally, I know myself to be a "fidgeter" someone who plays with his hands while working or listening. When I married I purposely got a textured ring so that it could be something for me to displace my energy and fidget with.