She might have thought she was a goner because of stuff like, oh, I don't know... all the huge attacks Pain unleashed against them.
Clothes are immune to damage... Katsuyu was safely wrapped in the clothes... so there's no reason she should have taken damage. This is under your own logic. Prove to me the chakra cloak actually touched her, show me the scan... and if it didn't, you have nothing but speculation.
Common sense of course just tells us she was shielded under the chakra cloak, much like Naruto and his clothes, but your fanboyism agenda forces to to find the least likely explanation to desperately try and give Katsuyu another feat.