Load your stacked animation GIMP file into Krita, group the layers which must be converted to an animation (multiple-select the layers, and hit CTRL G), and then select the group. Choose Layer, Convert, Convert Group to Animated Layer.
This will create a animated version of your stacked layers in Krita.
To play: Settings, Dockers, Timeline. Or switch to the Animation workspace (top right button below the close button in the interface).
To export to a spritesheet, use the spritesheet exporter script here:
https://github.com/Falano/kritaSpritesheetManager
Although I use TexturePacker for these final tasks myself. The free version of texture packer might suffice for your purposes. In that case just export all your layers from GIMP as PNG files, and drag into TexturePacker.
The big advantage of using Krita instead of GIMP for your animations: Krita has actual animation tools. And Krita loads GIMP files directly.