That may be tricky, if it's a solid glue line then it may also repel stain. You might need to sand a bit deeper and then skim fill with neutral timber mate or a tinted timber mate to cover and even out the surface. Not sure that using goof off or similar is advisable on a join like that.
The alternative is, if it doesn't bug you too much, leave it and see what happens when you stain it. Its a kit build after all, some of these things can just be regarded as character marks.