When I set up the 60g Anemone Cube, I knew I'd be using a Mp40w ES Vortech pump for flow, and that I would have to keep a sponge on the intake grate at all times.  Every few days I pull it off and give it a good rinsing because as it clogs up, the flow rate lessens due to restricted intake. Anemones do what they want when they want to, and you can't always predict their latest move, but you can protect them from themselves and the in-tank pumps. Find what fits your pumps and install one now, rather than after an accident occurs.

If you don't cover a pump and an anemone is sucked in, it may be possible to power down the pump and gently help the anemone extract itself.  Sometimes it may be possible to leave the anemone and the strainer section in the tank and the animal may pull itself out over a few hours.  

If the anemone is badly damaged, the nemocysts pumped into the system could kill corals and fish alike. You will have to decide how bad the damage is and implement a solution that helps the majority of the livestock.  The best choice is to cage the intake of any pump, or use a foam sponge to prevent the risk factor entirely as I do.