If you don't want to use them you're free to move them to the side for the game, as for removing them entirely/dedicating a few to malifaux, I'll ask.can you take them off the tables and put them away then?
The good news is that we've started working with Frontline Gaming to try and get some high quality proper playing mats in the store. They're sending us a few demo ones so we'll see if those are good and then will get more moving on.