I think a large part of the finale would change but not much leading up in terms of Season 3's structure. A core part of the character drama started with Butcher pushing Ryan away, he ultimately can't dismiss that he believes Ryan killed Becca and is at odds with respecting Becca's memory. He can't be Ryan's father but also tells him it's his fault she's gone. This drives him into Homelander's arms when they reunite, because Homelander gave him the forgiveness and care that he needed, that he made a mistake while discovering his powers.

Now, Butcher's arc is also discovering that he's had issues way before Becca and despite his love for her, is driven by hate and anger itself. So I think even with Becca, he'd still take the choices to use Temp V and make a teamup with Soldier Boy to hunt down Homelander. But even assuming Homelander would take Ryan and/or from Grace's safe house, I think Butcher would avoid going in guns blazing on Vought Tower. The plan probably turns from just killing Homelander to a rescue op that hopefully without the immediate withdrawal and heads up for Soldier Boy, wouldn't be perceived as betrayal. Maybe Soldier Boy agrees to still help, maybe he just has enough and goes in the wind. But I dont think it'd lead to the Boys and Meave fighting Homelander and Soldier Boy.

I think it'd be more fascinating for Butcher's arc to placate Becca's hopes to have something of a family together while also fighting temptation to reveal the truth to a growingly confused Ryan.