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.
90 Gallon Drilled Glass Tank w/ Corner Overflow: 492w (2x 150w 14,000K MH, 2x 96w Actinic CF) Coralife Aqualight Pro | Custom 34x15x15 Sump/Refugium | SWC Skimmer | Coralife Turbo-Twist 6x UV Sterilizer | Maxi-Jet Power Head w/Sure Flow Upgrade Kit | 120lbs of Live Rock | 100lbs of Live Sand