I too ripped my shin on the box last year. Talk about a blood bath, yeesh...
Learning to accept a longer time/fewer rounds for a WOD that involves jumps was the only way to proceed for me. My new gym only has those plastic, round edged steps, like for step aerobics, so adjusting the height is up to me. Did your trainers offer any alternatives to box jumps? Like step ups or lateral jumps? You could maybe pepper in a few box jumps if the alternatives are feeling too easy.
And maybe I'm talking crazy here, but would shin guards be okay to wear? I say wear whatever PPE you need to safely get though a WOD, and screw the haters/pretentious purists.
“Your task is not to seek for love, but merely to seek and find all the barriers within yourself that you have built against it.” Rumi