I really don't see what the fuss is about--there's no reference to any sort of gender roles here. Translated literally, it simply means "she is dirty, he is clean." Perhaps he just showered and she just got home after a long day's work? The fact that some people feel the need to infer something offensive says more about them than anything else.
Perhaps people are a bit too sensitive these days? Would people really feel that much better if it said "Ona jest cysta, on jest brudny"? Or would people prefer if every sentence were anodyne and sterile?
In colloquial speech you might come in from working in the back garden and say "Ugh, I'm filthy." but really you just have dirty hands. So there is definitely a very common use that refers to physical (un)cleanness, in UK English anyway. In fact I would say I'd rather use filthy when talking about people's physical state of cleanness. Saying someone is dirty has negative connotations beyond just stating the fact someone has dirt on them, for example that they have poor hygiene in general. Filthy is much safer in that it simply states that someone has gotten dirty somehow.
Note that both dirty and filthy can have sexual connotations, so i would say you don't need to avoid either of them for worry about this particular reason.