^It was both. Peter David rehabilitated Harriman in The Captain's Daughter and the short story "Shakedown" in the Enterprise Logs anthology, then David R. George III expanded on that Harriman characterization in The Lost Era: Serpents Among the Ruins.
I thought that GEN portrayed Harriman as a perfectly capable commander who was stymied by inadequate equipment. He came up with idea after idea for saving the refugees, and most of them would've worked if the ship had been fully equipped. He did show a lack of confidence as the situation wore on, but it was unwarranted, since his ideas were good and he did as much as any captain could in that situation. And Kirk didn't put him down -- just the opposite. When Harriman was doubting himself and ready to turn over the bridge to Kirk, Kirk refused and told him to stay in the command chair where he belonged.