Is that why it melted Madara's Susano clones in an open field? Lmao. She sealed the area to avoid damage to the other Kage, and she controls the pH willingly, so the pH won't be increasing at all.
At the end of the day, there's no reason to believe Kimimaro's bones will be immune to something which can easily break them down. Susano was broken down, so durability is almost irrelevant in exception of special cases I presume. But kimi does not fall into that category, so your points regarding chakra's molecules being easily broken are baseless conjecture at best.