I don't think there's anything inherently morally wrong about it, but I think it is a controversial thing to do because it is a power that could easily be abused. Instead of listening to the public, a government could just ask hold endless referendums until they get the answer they want.
It's not inherently morally wrong though, and I think there are circumstances where it would be ok. Scotland for example had a referendum relatively recently, yet circumstances have massively changed and are set to change even more, so a referendum would be justified. It's less about the time in between referendums than the state of political, social and economic circumstances; if things have changed then people are going to feel differently.
I'm also pretty sure another EU referendum would result in a remain vote.