Basically, socialism in extreme (communism) requires a metaphysically naturalistic explanation for physical reality (which must be the sum of all that there is in that philosophy). We see the same dogma in far left politics - leading to such initiatives as equal rights for animals, the right to terminate a child within a few months of birth, euthenasia, etc. all based on metaphysical naturalism.
Based on his wording above, I suspect he said what he did because it is true. If there is no evidence for a primeval soup and yet Marxists believe it exists, then they are like religionists standing on faith. He continues with the important remark that In science, the Absence of evidence IS evidence of absence.
Well, one of the reasons I am such an avid Republican is that I was trained by Marxists in college, so no one needs to explain "Dialectical Materialism" to me, I had it rammed down my throat by my commissars, oops! . . . ahem! . . . professors. But even the quote you offered equates supporters of abiogenesis with atheists, which still seems to indicate an agenda on Yockey's part.
I think your guess is right, A-G. I doubt that Yockey has a hidden agenda of some sort. It seems plain from his statement that what he's pointing out to us is that Marxism actually takes the form of a religion, a religion that is premised on metaphysical naturalism, which is the ultimate core and touchstone of its faith. The faith is consciously and deliberately intended to be a-theist. It is an attempt to explain the universe from purely natural causes. To the extent that proponents of abiogenesis tend to share this particular faith, they have something strongly in common with Marxists.
When you come right down to it, it seems that abiogenesis invokes the miraculous every bit as much as divine creation ex nihilo. Yockey's point may be that science isn't supposed to be in the miracle business....