Best advice I could offer after dealing with this exact issue in my current band is to simply get rid of the looper, and if not possible, get rid of the guitarist.
My guitarist, great guy, used one because when I joined the band, it was just a trio, bass, drums, and guitar. I have experienced first-hand everything you have talked about. It is the suck! There are so many variables and opportunities for a train wreck, that it totally kills the advantage this device might offer. I would say that it has its place if someone wants to practice a part or something, but NOT in a live situation!
I have had to play though one of my favorite songs against this evil device several times live. Something gets off, and then what the hell are you supposed to do? Do you follow the dumb loop, the bassist, what the guitarist is currently doing, ignore all and plow on ahead? And depending on the situation, and how well, and if you are monitored, it might not even be an option to hear what someone is doing.
They are just terrible. I can think of tons of three piece bands that got by without such a device or layered guitars, and they didn't sound empty.
Thankfully, we added another guitar into the mix, so bye bye looper!
Good luck brother!