If I'm working on such a job, and need to fill. I really hate having to resort to it, but if theres no other option, I get the dust out of my orbital sander bag and mix with white glue, until it looks and feels like a filler (if you know what i mean) I then wipe it on wherever needed and leave for 24 hours. It then sands nice and cleanly off.
Its hard to say really.... depends how big the gap is. If the gap is too big, then then joint has to be fixed properly. Sometimes filling with the timber itself can look alright too.