Great article!
It's difficult to say how much impact the fallout from Operation Rainfall will have. Most of the Wii audience will never hear a thing about these games or Operation Rainfall; however, I believe the impact of this goes beyond people who would actually purchase the games. I think the real impact is the larger audiences' perception of Nintendo's "talk to the hand" response. Even if I weren't interested in 2 of the 3 games being requested by OP's letter-writing campaign, this reaction from them has further cooled my own desire to purchase a new console. Nintendo's response on twitter and facebook was better than remaining completely silent, but their wording and timing of their actual response had a lot of room for improvement. Their first response, indicating that an announcement on the situation was forthcoming, gave tentative false hope, and their second was an equivalent slap in the face. (I think that they would have been better off just delivering the second statement without the first.)
The effect of this may be negligible, but we won't know for another year or two. The once-blue ocean is getting more red by the month, and it's difficult to tell from Nintendo's E3 messaging whether they plan to truly continue that strategy. Either way, Lindy is correct in asserting that Nintendo should be very concerned about their branding right now.
This is the first generation that I can remember where Nintendo has been repeatedly called out (in certain instances) for lazy development e.g. Animal Crossing, little to no effort advertising games, poor online store structure, lazy or no online in many of their titles, no support for their peripherals like Wii Motion +, etc. I've even got an impression from recent podcasts that the 3DS is really built all that well (for example, see episode 59 of the Newscast.) Rumors about the Wii U seem to indicate that Nintendo still plans to take the path of least resistance when it comes to online development. My own perception of Nintendo has changed dramatically since the Wii was released in 2006, and I don't know if I'm willing to fork out premium launch price for the 3DS or the Wii U at this point. I'm thinking to take a "wait and see" approach.
Lastly, it's a little silly to assert that any release of these games of any sort would automatically result in a loss of money. Atlus makes this sort of niche market work for them; so, again, why can't Nintendo just either emulate that style of marketing for games like this or hire a smaller company like Xseed or Atlus to take care of it?