ItsDan,
That’s certainly possible, but it overrides all widgets someone might be using. It might be rare that someone will want to display links in different ways on their site, but I have to err towards flexibility or else the plugin becomes useless for some. Maybe someone wants their links to be in a random order, but they want Link Categories in a specific order.
I hope the need to use a separate widget is offset by the fact that the My Link Order widget exposes all of the parameters unavailable on the built in Links widget. If someone needed to access those parameters they would have to muck around in their theme and figure out how to replicate their sidebar without widgets. A few years ago widgets weren’t nearly as ubiquitous as they are now, but it should be expected that a user can do everything with widgets that they can do with code in a template.