Working stranded knitting is not especially difficult back and forth. You just have to follow the pattern from left to right for the ws rows. I actually think that trying to knit them backwards would be a bit more difficult.
Not all Fair Isle knitting is worked in the round. It allows you to work large sweaters in the round, using steeks for the sleeves, though there are FI sweaters that are worked back and forth after the armholes.
For an afghan square, it wouldn't be necessary to work it in the round. Back and forth would be fine.