So if the dragons are called Jills, then if I kill one, do I get to use its meat to make a Jill sandwich?
But anyway, it's true that the name "Jill" doesn't exactly invoke a terrifying beast of destruction, but the name does predate Skyrim, and if these dragons really are Jills, I suspect that name would only be used in some dialog and lore, the actual creatures we fight will likely just be called dragons. And even if every dragon I fight is actually called a "Jill", hopeflly, the way they look and behave will make up for the unfortunate choice of name.
But seriously everyone, I don't think it was bethesdas intention to think of it as a girl's name.
That doesn't change the fact that it sounds like one, and since we naturally make that connection, when we hear it, we still think of a female name.