"seeing as how most of the non-crazy members ditched AVALANCHE once Fuhito grabbed power". Where did you get this information from, Mako? I've never seen it spelled out anywhere - namely, that there were TWO Avalanches in BC, one led by Fuhito and paid for by Rufus, and the other.... Somewhere, doing something. Fuhito, Shears and Elfe are the only leaders of Avalanche we ever see. Shalua Rui does eventually ditch Fuhito's Avalanche, it's true, but before she ditched him she supported him for quite a while.
Maybe I'm not making myself clear. In BC, which is the sole source of any lore about pre-OG Avalanche, there is only one Avalanche and it is led by the mad scientist Fuhito. There isn't a mainstream Avalanche and a lunatic fringe Avalanche. Fuhito is a Hojo fanboy who experiments on human beings, happily wreaks mass murder, and is as careless of the lives of his underlings as Heidegger. That is the established nature and modus operandi of pre-OG Avalanche, from the start of BC right up until the grand finale a mere month before Cloud arrives in Midgar.
Do we really think Barret would join such an organisation? Obviously, no one thinks that.
Which means there will have to be substantial re-writing of the Avalanche backstory. Either that, or they will just shove BC in a closet and leave it there. I don't think too many people would mind.
Nevertheless, I think it's possible that it was the Whispers and not Rude and Reno who blew up the Avalanche helicopter, and here's why: Cloud and Co could not be allowed to escape the Shinra Building via helicopter. That's not canon fate. And as we have established, the Whispers are the canon police. The party has to have their iconic motorcycle chase and their "final" showdown with Sephiroth.