Hi,
I never test this before, but you can try to first put the Value of 1 into the GPIO and then configure it as input, this should avoid a little bit the Glitch, but in fact, it is going to be, since the PAD, it is changing. Other advice would be adding a weak pullup, to see if this take the glitch out. If this is not I am afraid you are going to need another hardware solution.
Have a nice day!
Sol
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