No, she purposefully refused the surgery as she considered using it to become a "demon" as a short cut.
I agree though, the writers could have set it up much better to give her some kind of proper edge in this fight to explain how she gave "killer Mika" so much trouble, instead she's a lesser skilled pilot (and doesn't have the implant), in a way worse mobile suit, the only edge she had was speed on the suit (which gave Lafter the edge when she once fought Mika back at the beginning of the show), but even then shouldn't the Barbatos Lupus Rex be performing better after all those upgrades? The writers could have just done a better job making this outcome more believable.
Amida was beating her with her shitty mobile suit only a couple of episodes ago before she died.