Most pixel artists who work with a reference image are content to work with those images after they have been resized to the target resolution. You can then duplicate that on a layer, adjust the transparency, and lock it on top; letting you easily compare your pixel rendition to what the automated version produced.
I suppose one could imagine some detail that was lost... like a small yellow flower in a field of grass which became invisible in an automated reduction of resolution. One might theorize that if you could see the original image overlaid you'd notice the flower...then you'd put a big yellow dot in rather than the murky green that had erased it.
But practically speaking in the medium of pixel art, I don't think this comes up all that often. It might be a bit like asking for larger and more stabilizing training wheels, vs. learning how to balance on a bike. If you really need that yellow flower, you should be drawing it from your mind's eye, or at least be able to accomplish it by tabbing to another app looking at the larger image for a moment.
It's probably for that reason that you'll find it's a feature programs aren't busy figuring out trying to add. Tools like Photoshop and Gimp in particular aren't geared to working with hybrid resolutions in a single document. Layer content may have different dimensions...but each layer has to have the same "dots-per-inch", so to speak.
Even in Photoshop, the closest you'd get to a feature in this class would probably be a "smart object"...which although it has been scaled for display purposes, it is retaining whatever its original resolution was. And you can set the image interpolation to use nearest-neighbor. I don't know if Gimp has a comparable feature, and I'm also unsure if there's any way Photoshop could edit such a thing in place to make it useful for the "reference as you are drawing".
Despite the fact that you probably won't find a lot of interest in this feature, there are some third party apps that let you "ghost" one window on top of an other. You could load your image in a preview program and then match its size to the pixel art you are working on. For instance "Ghost-It":
Ghost-It runs in the system tray, and lets you turn windows into ghost windows. A ghost window is translucent and will always appear on top of other windows. When a ghost window loses the input focus, it remains translucent and always on top, but all clicks will pass right through it like it wasn't even there--until it becomes the active window again, either by clicking on the window's taskbar icon, or by pressing a user-defined hot key. You can configure the translucency levels of both active and inactive ghost windows, along with the hot key used to activate a window.
I actually have a fairly odd and sophisticated pixel art editor I'm making, and I suppose I could add this feature to it. Don't hold your breath for the release, however...it's a random side-project. :-)