Well Softy, I looked up Jim Downs of Connecticut College and he's a real legitimate historian but he is leading you in a direction he wants you to go.
"Many northerners were little more sympathetic than their southern opponents when it came to the health of the freed slaves and anti-slavery abolitionists feared the disaster would prove their critics right."
First, "little more" means they were "more sympathetic".
"Many" is a word used when you don't want to tell how many. 1000 is many but not is its 1% of the whole.
So MANY northerners were sympathetic. Yes SOME abolitionists feared the disaster would prove their critics right and SOME thought it was totally unfounded. Then we have that "some" problem.
See what I mean.
It turns out, looking at African Americans of today, that these fears were totally unfounded, no matter if the fear was based on the opinion that Black people were not intelligence enough to survive or the fear of a lack of skill, drive, whatever to survive.
From your article:
By early 1865 Miller himself was dead.
So bad were the health problems suffered by freed slaves, and so high the death rates, that some observers of the time even wondered if they would all die out. One white religious leader in 1863 expected black Americans to vanish.
The Civil War didn't end until 1865. Miller and his family were casualties of war. "One white religious leader"... ok who was he and why does his opinion mean very much, he's not a Doctor.
You are being lead down the path.
Consider this from Vanderbilt University:
The American civil war resulted in a stagnation of human development in the United States. The war was characterized by advanced military technology and inferior medical techniques, resulting in unprecedented casualties for both sides. As a result, the life expectancy in the United States between 1860 and 1865 continued its decline from the previous three decades. Between 1860 and 1864 the average American citizen would live for 40.5 years, and between 1865 and 1869, it dropped to 40.0 years (Hacker, 47). After that 5-year span, life expectancy began to rise at a steady rate again, averaging out at 44.5 by 1880 (Hacker, 47). Education, too, worsened during the war, as less people attended school in order to fight for their side of the country. While the total percentage of 5 to 19-year olds in school only decreased 2.2%, this was due to a 9.0% increase in the percentage of African-Americans attendance in school (Snyder, 11). White participation (white participation is measured because the overwhelming majority of both armies was white), however, decreased by 5.2% to 54.4% during the war and the years after, showing how education was secondary to the war in almost half of students’ minds (Snyder, 11). However, between 1870 and 1880, after the war ended, education became more important as 62.0% of white children attended school (Snyder, 11).
Your author was talking about a time span from 1862-1870. Here we have 1865-1869 the average life spans of all American citizens dropping to 40 years because of inferior medical techniques.
Consider this as well:
Seasoning was a process conducted during the Atlantic slave trade for the purpose of "breaking" slaves. It also took away the slaves' identities to make them more likely to do what they are told. Also during the seasoning process the slave would sometimes have hot tar and oil poured onto their sores and wounds so that they would fetch a higher price at auction.
The practice conditioned the African captives for their new lot in life; newly arrived African captives would have to be trained into the daily rigors that awaited them in the Americas. This training was carried out on plantations in the Caribbean, such as Jamaica.
Estimated mortality rates for this process vary from 7% to 50% with duration between one and four years.
Most slaves destined for island or South American plantations were likely to be put through this ordeal, though slaves shipped directly to North America bypassed this process. Jamaica held one of the most notorious of these camps. 
The process of seasoning had a strong profit motive. For example, the average price of adult male slaves in Jamaica (1770s) was approximately 52% higher than "New Negroes" (Africans who came to a New World).
"Seasoning" basically meant you held your slave for a "season", year, in case he died from the trip and the relocation. People didn't want to buy new slaves and have them die quickly.
Getting back to the song "Dixie". I have only recently understood what the song was about myself. I didn't have much of an opinion about it till I understood it. If Dixie said "the south is my home, its the best place on earth" I would not be offended by it. But it does not. It spins a story that was not true then and is not true now. It promotes the idea that slavery really is God's plan for mankind and that Black people will only be happy when they bow to God's will.