Assuming this STO developer speaks truthfully and isn't just creating positive spin, about why we should be grateful their game exists... something I'll concede might be the case -- taken at face value, it seems like Abrams & co would've had absolutely no problem going through with it, had a third party not objected.
I've listened to the relevant portion of the podcast now, and I don't think we can conclude that from what he said. He said that the game people complained about how the plan would scuttle the whole game, and then he said "So that got changed," but that "so" doesn't necessarily mean "as a direct result of our protests"; it could just be a conversational "so," in the sense of "then, subsequently" (as in "so then I said..."). In other words, they were worried, but then it got changed, so they didn't have to worry anymore.
After all, this guy is an employee of a licensee. He doesn't have firsthand knowledge of Bad Robot's decision-making; he only knows what he hears about it from his go-between (John Van Citters, I assume) at CBS licensing. So we can't make any conclusions from this account about why Abrams, Kurtzman, and Orci changed their minds.
Now, my own insights into the process are just as thirdhand as his, but here's what I know:
- It was an earlier draft of the film script that had the more destructive version of 24th-century events. Later revisions toned it down. (And yes, it was going to be in the film, not just in Countdown. Countdown took its lead from the future events referenced in the film script, basically just fleshing them out and adding TNG characters to them.)
- Kurtzman & Orci wrote the screenplay. As director, it would've been Abrams who was responsible for later revisions, particularly since the writers' strike limited the opportunities for the script to be revised during shooting.
- Orci is a huge Trek fan. Kurtzman is a moderate fan.
So the idea to totally trash the Prime universe most likely came, not from Abrams himself, but from K&O, who are fans of the franchise. And it was probably Abrams who changed it in favor of the less destructive approach. At least, that's how I've always assumed it happened (though, again, my interpretation is as subjective as the interviewee's). So I don't think it's likely that the idea was meant as some kind of "middle finger" to the franchise. I think, based on what I know about the original plan, that it was just meant to make the stakes for Spock Prime as high as they could possibly be. Maybe they just got so caught up in creating a big enough existential threat to drive events that they overlooked the fact that Spock Prime failed to avert that threat in his home timeline. And once that was pointed out to them, they changed it, or Abrams changed it. That happens sometimes. Sometimes you get so caught up in part of an idea that you don't see how it fits into the greater whole, or so preoccupied with the mechanics and details of an idea that you lose perspective on whether it's really a good idea. This is why writers have beta readers and editors and producers and the like to double-check their work.