Not knowing the song and with only this snippet to go from and assuming it is of an age:

"The captains of whalers are abolitionists
They go in for amalgamation;
A nigger or a Portuguese is treated like a man
But Americans are dogs on Desolation."

Which sounds, depressingly, exactly like the kind of nonsense you hear being whinged by racist, whites-first types in 2017! - Guest matt Milton

I think the meaning is very plain and totally at odds with:

"the verse given is clearly implying that the captains are snowflakes/libtards/leftists who are trying to destroy America by favouring the lesser races at the expense the poor oppressed Whites.

When was the song "Desolation" written?

No-one in their right mind would ever describe the Captain or Master of any sailing ship as a "snowflake/libtard/leftist. Onboard their vessel at sea as authorities they were second only to God.

The meaning of the verse quoted?

What was the purpose of a Whaling Ship? Rhetorical question - The ship existed to make money for its owner, the Captain and the crew, in that order.

Who went to sea in the days of sail? Rhetorical question - Those that HAD TO. - The Captains of ships struggled hard to crew them so they could not be fussy about who signed on that's the "amalgamationist" and "abolitionist" bits - anybody would do.

Who would the Captain and Officers respect most among those who made up the crew? Rhetorical question - Those who were experienced "whalers" (The Portuguese) and those who could work hardest without complaint (Slaves on loan?)

Why would "Americans" be treated like "dogs on Desolation"? Rhetorical question - They were the least experienced onboard a whaling ship, initially at the outset of the voyage they literally would be a waste of space and provisions, who knew nothing, and would not be able to contribute anything until such times as they had learnt the ropes.

Absolutely nothing to do with destroying anything.

Slaving songs: Congo River would be one.