Yeshiva Chachmei Lublin was actually given back to the Jewish community and is now partially a hotel and restaurant (Its also called Hotel IIan) , Its actually quite a large building and they have to make money to keep up the building (even so its a little worn down inside), You can stay at the hotel if you dont want to support the Poles, its main drawback is that its in Lublin which isnt where most of the places you want to go are (Lublin is 2-3 hours from Warsaw or Krakow) ,m However by staying there you are supporting the yeshiva that is there, they even do the Daf Yomi there now.
I do not know if there are any jewish guest houses in Warsaw or Krakow (Krakow is the main jewish area of Poland today) However given how many religious jews go to Krakow, it is possible there is some sort of jewish hotel there