"It's tough, full-speed, the whole thing," Harbaugh said, via The Baltimore Sun. "I hope the league really takes a look at this in the offseason and figures out a way to help the players out a little bit."
Reed, who earlier in the season had a one-game suspension he received for an illegal hit overturned, is likely to be fined, but not suspended, NFL.com's Ian Rapoport reported Monday.
The replay clearly shows that Reed tried to slow down prior to delivering the hit on Cruz, but was unable to completely change his hit point. He was flagged for illegal contact to the helmet and neck area of a defenseless player.
Harbaugh said the players are put in a difficult position by the current rules. He also pointed to a personal foul receiver Torry Smith received for an illegal block due to contact with his shoulder to the chest of a Giants defender.
"It's been a real challenge so far this year. Ed was trying to do everything he could," he said. "I could say the same thing about Torrey on the block back, it was chest high. Our guys are really trying to do the right thing and it's difficult at full speed to do that."
Follow Kevin Patra on Twitter @kpatra.