I'm basing my reply on what we knew before Marlyse, Marie, and Sarah were identified because the MC's DNA profile today is of a different caliber, for lack of a better term, as it was back then. I think it's a more complex profile compared to what it was initially in CODIS. I'm not a geneticist, so I'm probably using the wrong terms to impart her DNA profile is different now, not the genes, but the strength of it.
As of 2015, all they had was mDNA for all four of them, that's all they could obtain, their DNA was so degraded. That's how they were able to determine the maternal relationship between Marlyse and her daughters, though they didn't know the kinship at the time. And it was how they were able to eliminate the MC as being maternally related to the other three. According to the AG at that time, their profiles were not of the same standard or of a high enough quality to compare any of their other DNA to the criminal database to see if there was some sort of paternal match to known criminals. Marlyse's DNA was so degraded, they couldn't compare it to TPR's, once they had it, to rule out any type of relationship between them. And they weren't able to determine any paternal relationship between the four victims. Of course, this was all before three of them were identified and the MC's DNA was put in the forensic genetic genealogy pipeline.
Having said all that, I believe it would have been possible to identify a maternal second cousin when it was in CODIS. Definitely not a paternal one at that time. I don't know if they have re-run the newer profile through CODIS, though. I would hope so.