How can you have a Civ V "stack of doom"? You can't stack anything (except a worker/settler with a military unit but that's no help). I wasn't suggesting that CiV needs to allow stacking just that if you accidentally send your siege unit the wrong place through a misclick you can't send another unit to protect it (which is the solution I would use on earlier versions of Civ, though misclicks happened less often on those for me).
Though the best solution for the SOD problem I think would have been to return to the mechanics of Civ2 where if you defeat one unit in a stack all of them perish (there were exceptions for within cities and forts). That allowed you to have a unit that would protect from each unit category and yet give an incentive to not bunch all your units together.
After all rarely would an army consist of just one type of soldier be it cavalry, pikeman, tanks, etc. There would be a grouping of different types so that an attack of pikeman wouldn't slaughter the cavalry right away for example.