Pickups vibrating/moving minutely while playing has to do with the construction of the guitar, correct. However I hold it to the hardware rather than the wood to actually affect how the pickup moves (if at all). The mounting system will cover the large majority of whether the pickup moves or not, and the wood will still have a small effect.
I'm not one for anecdotal stories, I like evidence since I'm a science guy, but this debate would be extremely hard to win with scientific evidence. Anyway, my story. One night I was particularly p*ssed off about the tone wood debate and looked up videos on the YouTubez that were comparisons between guitars. Knowing that everyone who's ever watched a guitar video or played guitars has preconceived notions of how they sound, I decided to watch whatever video I found first with my eyes closed. I found a Les Paul vs. SG video. Perfect, I thought. I proceed to watch said video. There were no pauses in the playing to signify a change in guitar, it was continuous playing throughout. It's safe to say that I was thoroughly confused as to trying to decide what guitar he was playing at any point in the video. I couldn't tell for the life of me. I've always known Les Pauls to be a bit muddy, so I was expecting a distinguishable difference in sound. Nothing. Video finishes, I rewatch with my eyes open. Low and behold, I hear a major difference between the guitars now.
That's my argument for tone woods, really. EVERYONE has these preconceived notions of what certain woods and guitars should sound like, so they perceive that it does sound very much like that. I'm subject to this, all the time. I don't deny it. I get into arguments all the time with people saying "but why do my two guitars with the same pickups sound different, then?" Sorry, but is your brain completely devoid of any bias or preconceived definitions of what an instrument sounds like? No? Then I don't see credibility in your argument. You're destined to fail at convincing me tone woods do anything with your own anecdotal evidence - exactly how I'm destined to fail at convincing anyone with my anecdotal evidence of the video. It's each to their own, and in the real world, each to their own is not a huge issue in the guitar business really. People will be stubborn, all the time. The only real way to show some evidence would be to conduct a double blind test of people blind-folded or something while someone plays a variety of guitars. Even then that's not very scientific.