I tend to just make my SoD even bigger so at least some units come out of it unscathed
Troop limits per tile would be the only way to stop a Sod
I think there's a mod floating around here someplace where units in a stack in excess of some number (9? 10?) were all subject to a -10% combat penalty while in the stack. So you had the best of both worlds -- you could still move units through others without penalty, so there were no weird movement penalties, but you couldn't just pile on the units. Admittedly, I have not played this mod (I generally like to play the straight rules wherever possible,) but it seemed like this might be a good idea. Somewhat surprised that this didn't get implemented in Civ IV vanilla, especially considering how they were trumpeting the death of the stack of doom.
In fact, last night, I was paging through that Bradygames
Civ IV strategy guide, and it even says it in plain English: "The common
Civilization III 'Stack of Doom' tactic is now the road to oblivion: Collateral Damage has put this tactic in the ground." (p. 23). Alas, it didn't turn out that way.
To answer the original question, though, I will often send multiple stacks into enemy territory, but it's usually to pursue different objectives, and not to mitigate collateral damage -- with different stacks trying to either take multiple cities, or at least keep enemy troops pinned down guarding some distant city, while the main force drives on the true objective.