A giant toad-aided Fire jutsu would harm it. Not a normal one though. Not when all a mid-level Fire jutsu did was to annoy Samehada. You're overrating the Fire weakness.
Jiraiya's only shown the swamp jutsu with Earth, and we don't know if he has any other Earth Jutsu. I think he does, but I can say the same for Kisame. And considering Jiraiya makes a Swamp, most of Kisame's Water Jutsu won't be at a disadvantage.
Those stone swords aren't Earth jutsu as far as I can tell.
Which would likely be blocked by Samehada, as Kisame is fast enough to react to them. The damage from a Lariat and Bee's swords did little to really hurt Samehada.
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Stone swords aren't Earth jutsu. They're apparently swords from Myobukuzan.
True, but doesn't mean Kisame will not have any high level ones. He was at 30% of his strength at the time.
And again, higher ranked ones aren't necessarily indicative of inherent power.
__________________
"To all visitors from Transylvania looking for the head of Voivode Dracula: Yes, we have it. Yes, he's dead. No, you cannot see it. No, he will not return and invade you again. It has been over thirty years, please stop pestering us."