No matter what I tried, QT7Pro screwed up the alpha channel. I tried Photoshop... no help. I even tried iWeb (instant alpha wasn't available to animated gifs.)
I finally pieced together some info and... oddly enough, Preview correctly reads animated gifs.
You're probably not going to like this method (especially if the gif has several dozen frames or more) but it works:
Create an empty folder somewhere convenient (desktop)
rename the gif something really simple/short (for sanity's sake)
double click on your animated gif -- it should open in Preview [open the sidebar if it's not open] [If it doesn't open in Preview - right click on the gif and open with... Preview]
One by one: drag the frames in the sidebar directly into the folder you created (Preview will add the # of the frame to the file name + "(dragged).tiff" — it all works out perfectly since Motion reads file names like this as an image sequence and you don't have to Export or Save each frame separately.
Launch Motion (if you don't have it -- it's only $50 from the app store and you can use it for so much more [I hope you already have it because I hate recommending that anyone ever buy anything "extra" to handle a problem])
In the File Browser: navigate to your folder and you should see an Image Sequence, example: "FileName-### (dragged).tiff"
Drag the image sequence into the canvas
Resize your project to the size of the gif [click the Project "layer" and in the Inspector > Properties set the width and the height]
Set the project length to the number of frames *
Export at Current settings (should always be ProRes 4444)
It helps to add a Matte Magic filter to the image sequence and burn off a lot of those extra noisy pixels that tend to show up in gifs.
* You can use the Timing pane in the Inspector to set the speed of the animation and you can also opt to loop the animation in Motion for as long as you need before exporting. These options will figure into your project length calculation.
I converted this (Realistic-fire-animated-transparent-gif.gif on Photobucket)
and got the transparency in FCPX:
(just a still -- it really does animate)