Not talking about games specifically, and it's no wonder that there's outrage at games since games are only a small part of both franchises (similarly, D&D computer games aren't as significant of a part of the franchise as a whole). Although I've seen plenty of outrage at e.g. the Bethesda-published Star Trek: Legacy. And as I said, the reactions to the new X-COM game are similar to the ones to Fallout 3. It happens in pretty much any franchise where one style is completely replaced by another.
His input on FOT was not as significant as he'd want, as he himself said in some interviews, unfortunately (e.g. he asked them to make the looks of power armor etc. more retro, but they didn't). And unlike with FO1 and now FOOL, he did not work directly on the project (Microforte did), only supervised it to an extent on Interplay's part. He wasn't the one "violating the setting", you could at most say he wasn't effective enough at stopping others from doing it (then again, Herve wanted it out of the door as soon as possible, which meant there wasn't much time for major changes).
Nope, he wasn't limited to the technical aspects (although that was his main area of work). He e.g. designed New Canaan, and acted as lead designer after MCA's departure.