I had similar concerns. I have read threads where people insist that copepods are going to get diced up in the return pump. However, most people that keep a refugium for the purpose of copepods report that the return pump causes negligible damage if any to the copepod population. I have also been in correspondence with Dr. Adelaide Rhodes from oceanpods.com . She is an expert on copepods. She did not believe that a return pump would be a concern. This was her response when I asked the same question: "When people are concerned about copepods getting chopped, they are probably referring to the species with long antennae. Honestly, most copepods will swim against the current or cling to surfaces. Any harpacticoid copepods that pass through which have small antennae will make it. All of my species are harpacticoids, which are compact, torpedo-shaped bugs."
(to me that another good reason why not to try to populate your tank with tigger pods. They are bigger and probably have more of a chance at getting chopped.)
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The message above from Dr. Rhodes. She says all of her species are from the harpacticoid family.