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It is worth a try. Being a military bank you would think they understand deployment hardships.
I would try sending them a message via the website. A couple years ago, I had a nasty string of overdrafts over the course of a week when I had a death in the family and was high on pain meds from a nasty kidney stone. I sent them a message detailing the situation--they reversed every single overdraft charge and vowed not to add any more until I was able to bring my account back into the black.
While I understand this is different from asking them to remove a late from your CR's, it's also different from being out on deployment. They can be pretty empathetic. I think you're more likely to get a positive response via message or email; there's not that pressure to keep call times down weighing over the CSR's head.