Personally I would leave the chair rail in place, first off because like was mentioned before it does add structural strength, and second because you can use it to mount other things inside... I have some seats I got from an old 727 that I'm planning to use the chair rail to connect the back of the platform they will be installed on, which will be hinged at the front so I can use the space underneath for storage, or maybe I will put my water heater and/or water pump under there, depends on how much room there is. But I digress...
You could use it as an anchoring point for cabinets or anything else you want to have in there. Not the sole anchoring point of course, unless it's something that will sit low to the floor, but useful all the same.