Definition: to stand in opposition to
Why I Looked It Up
William F. Buckley famously said:
A conservative is someone who stands athwart history, yelling Stop, at a time when no one is inclined to do so, or to have much patience with those who so urge it.
Added on August 28, 2922
From the novel REAMDE:
After a few agonizingly slow and controversial minutes of this kind of progress, they came athwart of an alley, no wider than a doorway, on their right side.
In this context, I think it means “perpendicular.” The characters were in a van at the time, and so they would have been across the opening of he alley.
Indeed, Merrium includes this as a definition:
across especially in an oblique direction