I don’t know exactly what you are talking about, who these “pirates” are, or who’s station (citadel, presumably?) they attacked… but…
Preventing your enemies ability to produce things will undoubtedly hurt them in a number of ways. Stop them making ISK. Make it harder for them to replace lost assets. Maybe even hurt their morale and get their industry people looking elsewhere for the services they need.
Usually hurting the enemy’s economy and ability to make ISK is far worse than any military victory on the field. Losing ships in battle is nothing in EVE any more.
Why is it impossible to stop the work started in order to use the slots at another station.
When a Citadel goes into final timer (structure timer) or otherwise goes low power (due to running out of fuel, for example) all industry jobs are automatically paused. - I can’t remember if the user can then manually cancel them. I suspect not; that they are frozen until the service comes back online or the structure is destroyed. (Correct me here, please, if you know better.)
Either way, if you cancel a job you don’t get the materials back, so you lose ISK by doing that. So if you are doing anything big, you definitely will want to try and resume the job where it was started, rather than take it elsewhere and start all over with new materials.