I’ve used the invocation
scribble --prefix my-prefix.tex
with a file my-prefix.tex
that starts off
\documentclass{book} %% You could use whatever class you need here
\PassOptionsToPackage{usenames,dvipsnames}{color}
...
I’m not sure whether you’re trying to actually use those two settings and there’s an inconsistent load, or whether you’re trying to actually not use those two settings and can’t avoid them. My solution fixes the former kind of problem.