He was a mess in the desert.

[It's been six months, but they have no way of knowing if he managed to pull himself together since.]

I think that Darcy won't let him protect her if she punches you in the face. She's the type to want to beat someone into submission on her own.

Anyway, it just means that Dedue doesn't want Skulduggery murdered, not that he agrees with him. And since murdering Skulduggery means retribution from the captain, one passenger's declaration isn't going to change things.