You have made the incorrect assumption that there are only 2 scenarios that assume people commit 100% either way. What would happen some developers make good on the CCP/Revision, some will outright forgo support, some would half ass it, others didn't get the memo. I don't know how many devs would fall into each category. All we know is that your assumptions are incorrect, therefore your scenario(Strawman) is bunk.
History shows branching hardware when it comes to controls isn't fatal. It not just Dual Shock, look at the Wii with it's Wiimote, nunchuk, classic, GC, balance board, Wiimote plus, dual Wiimotes. Based on the assumptions made in this thread, the Wii should be a corpse the moment it came out.
We already have "Second class citizens" on the 3DS, they are called left handers. I am not one of them, but I can imagine how aggravating it can be. Increasing accessability is a massive positive when it helps you make inroads in a normally forgotten 10% of the population.
In a revision, supporters of the previous system have the option of upgrading for a fairly reasonable price. I got my CCP for less then $10. It's cheaper than a normal controller and you only need to buy one.
The question is whether Nintendo is going to formalize CCP support, continue on it's current current stance which is best described as Laissez faire or abandon it. The CCP exists and it opens the door for Nintendo to make a revision to include it.