the loss of Chris Avellone alone was a huge blow
I'd have to question that. In retrospect, and from what leaks I've seen here, my reading is that he was already sidelined in New Vegas, and then completely sidelined after Alpha Protocol.
Alpha Protocol was released four-and-a-half months
before Fallout: New Vegas, which itself was followed by four expansions, with Chris Avellone as the project director for three of them: Dead Money, Old World Blues, and Lonesome Road. Chris Avellone was only sidelined on F:NV because he had already been tasked with bringing Alpha Protocol to completion.
However, it does appear that, as a consequence of Alpha Protocol being a commercial flop but Fallout: New Vegas a considerable success, FU decided to sideline Chris Avellone on future game projects, while placing Obsidian's future in the hands of his new golden boy, Josh Sawyer, with predictable results.