If need be, first square off the very uneven surfaces by sanding away some of the wood, and building it back up by adding fine strips of balsa back in its place. The CA'd surfaces are going to be stubborn to sand easilly. If they are too uneven to work with, I'd just completely sand those CA surfaces away to the fresh soft wood.
To do this for example, you can remove about a 1/8" of wood on the hatch, and a 1/8" of wood on the frame that the hatch fits into. When you've filed or sanded to make the recesses nice and square and perpindicular to each other, proceed with glueing and filling new 1/8" sticks back onto each surface. You sand them lightly with 400 sandpaper until it mates up tight and neat. By trial and error you keep sanding off a little wood with each stroke of the sanding block until you've got the surfaces mating up very square and close to each other. It's not unusual to find that you might have sanded one surface a little too far and produced a 1/64" gap for example. So you just glue a little balsa splint back in place and try gently sanding again until you get it to mate perfect.
The fine remaining gaps and crevices can be filled-in almost completely with epoxy. CA with filler is not what you want to use because it's too hard to sand, and dries too fast to shape or work with.
To fill gaps with epoxy; take the completed hatch out of the frame.
Rest a square of Saran wrap over the frame. Now put the hatch back into the frame. Ok, now you've got saran wrap sandwhiched in between the hatch and the frame, right? Tightly pull the saran wrap back over the hatch to cover it, and now tape it down taught, stretching it tight out of the crevice you're going to work with. Now you can mix up a little 5 or 15 minute epoxy and fill the frame gap with it. But first, you need to first mix a lot of micro baloons with the epoxy to really thicken it up, or it will run and sag too thin as it hardens.( I've heard you can also use baking soda, if you don't have micro ballons powder.) You use your finger tip to wipe away the excess epoxy off the surfaces of the fuse or wing( or wherever the hatch is located)before it hardens. If your skin is sensative use a rubber surgical glove. When you've pulled the saran wrap off later, you will have a very tight fit.

It's hard to tell exactly how rough those CA crevices are by the picture. But you might be able to use them as is and not replace the joints with fresh balsa. You might be able to fill the rough gaps with the epoxy process alone. The problem is, if your gaps are too big, the epoxy will have a tendency to settle down into them. Then you will have to, do the epoxy process again and again until you finally build it to the top surface you need. If you try to use plastic wood or balsa filler in such small amounts in crevices or gaps, it will chip or flake off. So use the epoxy.