"support for the overthrow of the United States Government," is also one pre-crime per that report. That's reflection right there.

So Marx and Trotsky seemed to be against individual murdering of factory owners et alia. Does that imply that they would've been against the atrocities of Communist states that were perpetrated in their name, or would that have been fine because it was done by the masses in some sense?

Neither saw it happen in great numbers: Marx died before any of his ideas manifested properly, and Trotsky of course was murdered by Stalin in 1940. Holodomor and Soviet Union purges had happened already at that point, but perhaps Trotsky might've thought that those were just the evil of Stalin instead of being a more general mistake of his whole ideology. People tend to think that their political philosophy cannot do bad things.