No one cares about insults to Geodudes. The part that's getting a reaction is the implication that "half" means the same as "autistic or special needs." It's in the same vein as if you had said that the half Geodude was a female or was a darker color than the full Geodudes (those too would be offensive regardless of whether we're on the surface talking about Geodudes).
I try to rail against excessive PC culture, but this doesn't seem excessive IMO. This is similar to jokes that have belittled as much as half of our population for centuries as a means to "keep them in their place." Changing the target doesn't change the overall issue.
For my part, I'd like to drop the discussion now. I think we've covered why people could/would have a problem with the joke, and I think it's pretty clear you didn't mean the joke in that way.
Let's get back to Pokemon