I don’t think you read the NY times article...only the San Antonio article.
They were traitors and were going to Mexico so that they could escape to New Orleans to join the union army.
Why would they join the Union army and kill confederates? Peaceful people yes?
Why would they join the Union army to kill Confederates?
Perhaps because their allegiance lay with the Union, not the Confederacy. It could just as cogently be argued that aligning with the Confederacy would have been treason.
In any case, these immigrants were forced to either declare for the Confederacy or face extinction. They made their choice and were murdered as a result.
The South was capable of far nobler treatment for dissenters. And there is no justification for the wholesale slaughter of civilians with whom you disagree.
Two months after this 40 Unionists were lynched in Gainsville, Texas. Maybe these were peaceful people who saw the writing on the wall and were trying to get out of Texas while the getting was good?