Luffy handled it badly. He just suddenly says they're changing ship, with no discussion. Usopp was the shipwright who'd put thoughtful craft into the ship, so it should've been discussed with him there.
Usopp was working with knowledge that Luffy didn't have, since he was the only one aware of Merry's spirit. He treated it like a living thing and believed in its power to overcome hardship and limitations put on it by others, just like Luffy would about a living person. If Luffy knew what Usopp knew, he might've found it harder to move on too.
Usopp even says "I can't leave behind a wounded comrade" and Luffy says "That's stupid. Ships and people are two different things", which shows the difference in how they see it.
In hindsight Luffy was right to stop using the Going Merry, because even with its spirit the ship wasn't fixable and did break. But Usopp's belief in the ship is what saved them from the Buster Call.