That's not his ability. He can't affect ALL molecules. Just water and air to create ice.
There's nothing about it that would make some sense of him removing magical properties of a sword by encasing it in a layer of ice. It's poorly thought out crap is what I'm saying.
Maybe his ice is colder than normal ice ?
I see it a bit like Yamamotos bankai when he was younger - "Bach" was suprised that there were no flames around Old Man when he activated his bankai and we seen painting of Yama being on fire. So I guess it worked same way as Hitsu current state - having pretty wide area of influence and burning all around him to crisp.
Beside, poorly thought out crap in world of souls ? Maybe spirit energy can be frozen? How can you tell?
I hope you get what I mean. Are you really nitpicking because Bleach doesnt follow real world physics?