If there's anyone Gaius would be vengeful towards, it would be the Ascians, not us. We beat him fairly in combat and he even acknowledges that we did so after we leave at the end of the Praetorium. The Ascians though? They lied to him about what the purpose of Ultima Weapon was for and played him for a fool. If they had told him the truth about Ultima Weapon's purpose, he probably would never have used it. He hate their guts.

If anything, we see this playing out in 4.3 and 4.4. Gaius is essentially doing (or trying to do) what we were doing for all of 2.0. He's going after the Ascians which is what the Scions and us were doing back then. The Praetorium revealed to him who was right and who was stronger when it came to the Ascian conflict and that would be us. Gaius letting us do whatever we want while he goes off hunting down Ascians in places we can't easily get to (Ilsabard probably) fits in nicely with his philosophy of the strong ruling/leading the weak.