Once when I was trying to apply JJ to an Aptasia, my cleaner shrimp snuck up behind my hand and jumped on my had, I wasn't expecting it, so I jumped and globbed a bunch of JJ on the aptasia, and rock work.
I never turn off my pumps. I didn't have any problems with my corals.
I think you'd really only have problems if you injected it right ontop of the corals. But It never hurts to be safe.
-TheChad