The whole reason I even have a carry-on when I fly is for those items that are too valuable and fragile to be checked. In my case, that's mostly computer and camera gear.
Having seen a few instances of people being forced to gate-check their bags, I am now paranoid about it and go to great lengths to make sure I board early enough to secure overhead space. If I'm ever delayed or hit with some other circumstance that forces me into gate-checking, I think I'd probably do exactly what OP did and eat whatever charges are necessary.
Of course, if that happened, I'd also complain incessantly to the carrier until they refunded any extra charges I had to accrue.