If you use that pattern, the color work is pretty manageble, because mostly it is one by one changes and then the big blocks. You will need to weave the back side, though, because long strands floating along will not make a nice scarf. (check my blog for how I do it, there are videos telling the exact way, if you knit Continental Style, and I did collect the links, as well, that are for both methods and English only.
But if I were you, I would work that scarf in the round, as well, since then you will not have an exposed backside with strands, floats or woven strings.
I have seen knitting (no pattern, though), where for the "mix-color" part, all stitches are done with both colors running together. If you do that, these sections will, of course, be a different gauge and thickness, but it may pay out. The bigger the needles are, that you use, the less this will actually show, as far as my thinking goes...)
If you work like that, intarsia might be your friend when working back and forth (intarsia just does not cut it in the round (unless you are insetting just very small pieces that you can "backtrack" on).