How can I deal with non square walls when installing a countertop with backsplash?
If you are installing a tile backsplash, just sort the issue out on the tile substrate. Depending where you want the tile surface, either overlay backerboard and shim to correct the gaps, or rip out the current wall surface and replace with backerboard, shimmed to correct the gap once the tile is installed (which may mean an even gap before the tile is installed, again depending how you intend for it to look.) 

It's a small area, should not be too difficult/lengthy a process.

Counter looks a wee bit high going by the window opening...if that's an egress window you may fail inspection for partially blocking it.