You're correct about the released version, but I was talking about the leaked pre-release outline -- the one where the name "Catalyst" hasn't been invented yet and the intelligence on the Citadel is known as the Guardian instead, (My fault for being unclear about what "original ending" meant.)
People said that destroying other AIs was a late addition to make players have to consider picking something other than Destroy. People were right.
I do apologize for the oversight of the word "leaked"... However, I would be hard-pressed to say that there was no intention whatsoever to include AIs in destroy's casualty list. If you have read the leaked script, you would notice that all the consequences are reaper-centric and that synthesis seems like a half-baked idea which most definitely requires more definition and refining.
My opinion is that the devs simply had forgotten the many consequences which may result from a galactic explosion and admittedly hazily rushed to add more things to the endings, but the point I made above may only be refuted if you can prove that the leak directly caused the changes, otherwise we could never know whether they were intended or not
EDIT: Or, this can be interpreted as a timing issue, whether BW intended AI casualties in 2011 or they intended them in 2012 is irrelevant, we know that these consequences are intended because they ARE included in the original ending and that more importantly, they are still included in the extended cut and not removed