In the Pale Moonlight was not Prime Directive. First Sisko had permission from his superiors, and second, the Federation and Romulus had been to War. How they treated each other was decided by treaty. The Treaty of Cheron where the Earth Romulan War stopped, and the Treaty signed after the Tomed Incident in 2311.
What Ben did was scummy and broke some laws, but I doubt the Prme Directive was one of those laws.