We use clean disposable paper coasters that are used for sitting drinks on for cleaning our wine glasses, we never use the towels to polish glasses. And usually what we do is when we find lipstick still on a glass after it's been washed, is wipe off the lipstick with the paper coaster, and then put it through the washer again.
I'm sure it's still not ideal, but we'd never use towels to clean any kind of dishes or glasses, they're just used to wipe the bar down and at that stage they're saturated in sanitizer. Glasses and dishes are washed at such a high heat, that they are practically air dried as soon as they're taken out of the dishwasher.
Our work kitchen is probably the cleanest I've ever been in, it's scrubbed top to bottom every night, and the kitchen staff are really clean. It's one of the reasons I don't mind eating in there as much as I do!!