I am most definately not sure if it is the Thalmor that should lead this charge as they usually have their own agenda in mind. Admittedly, if they could pull it off, it might be a very strong chink in the Nord armor. On the other hand, in the end, the Thalmor and the Falmer are far more closely related genetically then they ever would be to any Nord.
While I can understand why the Nords have issues with the Falmer, it is perfectly within character for a Nord to be racist against a Falmer.
I never really thought of the Falmer as being stupid animals and always felt slightly guilty about slaughtering so many in the Dwemer ruins. What are we (the surface dwellers) really using all these ruins for? We use them to make a profit. Even if we say it's for "research", in the long run we come out with tons of booty and make money. The Falmer obviously have their own society, and have a very interesting relationship with many of the undergrounds denezins.
Maybe, if we gave the Falmer the tools and left them alone (do we really want to be living in their underground anyhow?). With a noted lack of Dwemer about, I am sure they could slowly become something more than they currently are.
Personally, if I could build a relationship with a Falmer, I think it might be interesting to get their world view, learn about their society and see just how we as surface dwellers might fit in.
I know this sounds naive, but I am not a lore-master and can only judge on the behaviours and situations of which I have experience.
Lore and histories are written from the writer's point of view and are coloured by that writer's personal dogma and experience itself.
Let's just stop slaughtering the Falmer every time we see them, give them a leg up and, maybe, just maybe, eventually they can come in to the light and be comfortable with it.
By all the 9 though! Don't let it be the Thalmors that organize this! It will lead to nothing but tragedy for everyone that is not Thalmor.