The simple reason is it was a cheap fix. The Magic Mouse used to be powered by 2 AA batteries which sat behind a panel under the mouse. When they moved to it being rechargeable they simply swapped this area under the mouse for a rechargeable battery with a port to charge, the rest remained identical. Adding a charge port to front of the mouse so you could also use it while charging would have required a redesign of the mouse as there isn't any way to place it.
Had the Magic Mouse been conceived as a rechargeable device from the start it would likely have been designed differently.