This would be standard behavior on ANY powered USB hub. I have 2 hubs in my office, exact same thing. You'll have to adjust your workflow if you don't want the drive spinning up, but as long as there's power to it, it will run. And that has nothing to do with the Surface Dock.
As above, hence my previous post. It is a powered hub, it is doing what it was designed to do. Maybe it was not designed "well" in that maybe there could be a switch on the dock to turn on and off the usb power, but it's the way it, and nearly all, are designed. Possibly for a good reason.
And to me, the dock is not to stop me having to plug in or unplug a cable, but rather 4-6 cables (audio, power, usb hub, dongles, video) and the inevitable tangle all those cables will eventually create. I'd have no issue unplugging one usb cable.
Also, you'd have to take action to turn off the usb power, which in terms of effort and time involved would be very little different to just unplugging one usb cable.
Yeah, for certain people, such as yourself, it is unfortunate. But it is essentially nothing more than a powered USB hub with the addition of network and video output.
I imagine part of their thinking (despite marketing the sp3 at students!) Is that people buying it and the dock are professional, with a separate office space aside from their bedroom, so noise or blinking led lights are irrelevant. But as you have experienced, not everyone has that luxuary, especially students, so it would be nice to have a little switch on the back to cut power to the USB ports. Or just a switch that turned off the entire dock features other than powder to the surface.
Maybe you should email ms. It is a fairly genuine issue IMO and hardly beyond the realms of possibility to ammend.