You're still cutting a take off and landing so I can't imagine it'd be too hard to break even for flights where this increased capacity is helpful.
Not having to land but instead having to carry some extra fuel while the engines work in their most efficient mode, and the air drag is low at a high altitude, should make airlines money. Else they won't try that :)
So even if you only care about carbon emissions, it can still make sense to skip the stop even if it causes slightly more total fuel burn.
Armchair experts won't correctly estimate all of these incidental costs nor the value of the saved time and overhead for everyone involved.