Whoaaaakay, Mobius. Slow down, take a few breaths.
People can come up with whatever theories they like to explain these inconsistencies. And, for now, that's what they are: inconsistencies.
Because at no point in FS2 did anyone actually come out and say 'the Shivans have always had beams, they had them back in the Great War'. Nor did anyone say 'There was only ever one jump node to Sol.' As Snail said, it's hard to find a single statement that retcons FS1.
Inconsistencies were ignored or glossed over, but no one came out and retroactively changed anything. So were there any actual retcons? Arguable, I guess.
If Volition had made a point of retconning in the story, we'd know, because it would be glaringly obvious: 'The Shivans have always had beams.' As it is now, you can read it either way.
Maybe those pilots attacking the Behemoth weren't surprised because the Shivans have always had beams - a retcon. Maybe it was some other reason.
But there's just no reason to force this idea down the community's collective throat. Why not let people do their thing? There is no Freespace fanon, and there's no need to create some crazy set of rules a la Lucasfilm Licensing.
Lastly, what do you mean retcons aren't canon? By definition they supersede and replace existing canon. They are certainly canon.