The important thing to understand is that when you do a merge, you're only merging the duplicates of one person, not a whole family.
The act of merging does not create any new duplicates. It just sometimes brings them into the same family. For example, if you merge two profiles for John Smith, and each of those profiles originally had all of his children, then once the John Smiths are merged, all those children profiles will have the same father. So when you look at the combined profile, there will be twice the number of children. But those profiles were already there. Now they're just easier to find.
So, merging is still an improvement. It might make one profile look messier, but only temporarily, until the family members are merged. And it's still a step in the right direction for cleaning up the tree.
I hope that helps clear things up!