As I understand it now, the main reason we can't have animated gifs in roll20 is because of how the system renders everything. In simple, the engine renders everything as one large image, then your viewer only renders what you are currently viewing. Because of this the first frame of GIFs are only shown.
My suggestion is to render the GIFs as their own layer and objects. I do not know much of how HTML5 works, but from what I do understand it should be possible to render the GIFs as individual objects on top of the the main maps image.
I can foresee this not being added for some time though due to how complicated it might be.