It wouldn't have made a difference in the last few elections because Labour have been so poor but in 4 years time, 9 years time, 13 years time, who's to say there won't be a Labour Government?
If they do become separate, what will happen if these voters don't get their chosen government in Holyrood? Are they going to split again? Are the Orkneys or Shetland islands or Glasgow going to go it alone?
At some point, you just have to accept that you're not gonna get your chosen government all the time and part of living in a democracy is accepting defeat.