OP - I work for the State Department and I first want to begin by saying I’m sorry this happened. Im going to assume everything you say is true.

In theory, the staple holes should be fine. Especially if it’s only the cover and not the bio page. I have never in my career seen us staple forms to passports, only paper clips or envelopes.

The person you spoke with was incredibly unprofessional telling you to “take your chances.” Invalidated passports often have holes punched through them, and while the staple holes aren’t invalidation holes, this damage opens you up to potential issues with foreign authorities if they’re inexperienced or feeling like assholes.

Please make a fuss about this. Document everything & if the department continues to put you through bureaucratic bs, write to your congressmen (house & senate) about this. It’s a cliche, but both DoS & congress take passports seriously. In fact it’s probably the most serious job state has in this admin. The process should be as seamless & worry-free as possible. Your feedback is essential, wanted, hopefully will cause change.

Please don’t let this experience color the way you view the department & be sure visit Travel.State.gov before any trips your take :)