Given Marx's view on labor and the working class one could hardly expect him to side with the proponents of slavery could you? But other than recognizing he need to end slavery there wasn't a lot that the two men agreed on.
They both agreed on big government. Big government isn’t effective if people can just walk out of it when it starts to crush their freedoms. That is why Marx and Engels supported Lincoln’s push to create a “single and indivisible republic.”