"Popular Sovereignty" seems to us today to be more sympathetic to the South, but it was deemed not sympathetic enough by the South at the time.
However popular sovereignity wouldn't be contrary to Dred Scott at all. Theres an important distinction, popular soverignity would allow a state to decide when it asks for statehood...…..prohibiting slavery from the territories was an attempt to preclude the possibility of a slave territory asking for statehood as a slave state altogether, the territories wouldn't have the opportunity to see if slavery was suitable or advantageous to the territory at all, even though it was a legal practice in the US.
I think there is a distinction being missed here. Popular Sovereignty as initially derived was not viewed unfavorably by the South in general, as it initially arose out of the 1850 Compromises allowing Territories to decide at statehood.
The problems arose out of the Kansas-Nebraska Act and the subsequent Dred Scott ruling that followed. The Court essentially declared the old Missouri Compromise unconstitutional and that slavery was protected in all the Territories, even above the old Missouri line. This “protection” aspect of Dred Scott becomes important.
And this is where the non-intervention doctrine entered the scene. If Dred Scott declared slavery protected in the Territories until Statehood, who or what will enforce that supposed protection?
Douglas said that Congress should play no role in either protecting or hindering slavery in the Territories.
This was troublesome to the South -and understandably so. Money and investments gravitate toward stability. Without assurances that slave property would be treated and protected equally in the Territories as other property, who would take the risk of moving vast and valuable property into the Territories?
Douglas frustrated this with his Freeport Doctrine, or what the South would call “Squatter Sovereignty.”
Under this policy, a Territorial Legislature could do indirectly what the Constitution and laws will not permit it to do directly. In other words, if a Territory really did not want slavery, then it could resort to unfriendly territorial legislation that could essentially prohibit or severely limit slavery in the Territories long before it ever sought Statehood.
This is the “popular sovereignty” of Douglas that the South opposed bitterly. It had changed from the 1850 concept. To them, it essentially operated to remove the rights of Southern citizens in the Territories as guaranteed by Dred Scott or the Constitution.
Douglas would not back off this non-intervention interpretation of Dred Scott or “squatter sovereignty” at the Charleston Convention. To Southern delegates, this policy simply denied citizens of the United States equal rights and equal protection in the Territories and so they seceded from the National Convention in protest.
The Republicans were explicit, they did not want slavery in the Territories and they proclaimed it loudly from the mountain tops. From a Southerner’s perspective, Douglas was just being sneaky about the whole thing, trying to hustle them into voting for something that would essentially do the same thing as the Republicans wanted.