The show's writers have a LOT more control over the show than you seem to realize. Hasbro doesn't come in and call the shots. They just sit there, waiting for the product to be brought to them, then approve it if it's up to snuff.
You can't honestly believe that there was zero forced input from Hasbro on this one.
H - "We want to sell a Twilight Alicorn toy, make it happen in the show!"
W - "Well, there goes our plans for the future of the story. Now we have to tweak and edit and alter our overall story starting now and for all future episodes for the sake of this toy."
Not saying that the writers wouldn't have eventually gotten there, because you can see that's where it was going. But, they (H) wanted it and they wanted it NOW; not next season with several episodes building up to it. Most likely they came up with the idea for the toy while S3 was in production and said "forget what you wanted, put this in S3." Not saying that they can't make it work, because I know they can.
And I'm not limiting this to just this one show. There are hundreds of shows that are forced to sacrifice story quality for the sake of ratings/advertisements/InsertUnjustifiedCorporateReasonHere and I personally hate when that happens. Just another example of the suits screwing over creativity for a buck.
Not trying to argue that it shouldn't have happened or anything like that; I see the potential for future episodes with a change like this. And, personally kinda glad to see someone get rewarded for their hard work instead of being thrown aside and forgotten. Can't help but find it appropriate that it's happening in a work of fiction though.