To the best of my knowledge, a snake's glottis closes automatically when they're in the act of swallowing. Plenty of snakes take on prey in & under water, & while ball
pythons aren't usually one of them (due to environmental differences), I really doubt that you have anything at all to worry about. Wrestling prey will cause a snake to
breath hard...it's not as if your snake is an athlete that regularly works out, lol.
I've been keeping lots of snakes for many years...I've never seen a snake have any sort of problem like you describe, & in fact, my most aggressive feeders include my
large adult FL rat snakes that are often on their branches when I offer them f/t rodents, & they're so enthused trying to "kill it" that sometimes they fall off their branches
& hilariously right into their large water bowls. They may or may not get out to finish eating, & none have ever had a respiratory problem...so I'd say "relax".
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