This does all depend on how big/small the gap is. Really if the gap is bigger than 1/32-1/16" it will be noticed no matter how you fill it.
Most of the advise I've read, and what I would do if the gap were to big is route off the binding and purfling and redo the channel, making a different purfling scheme if needed.
Sorry for this advise, but you may never be satisfied with the guitar if you choose to fill the gap instead of making it right. I know this can be hard advise to hear, but it's your guitar and only you really know how you want it to turn out. That is the dilemma sometimes. If this is your first guitar and you feel like it won't be an issue for you, use Hesh's advise and fill that gap, or if you just know in your gut that you will always look at it and say "I wish I would have fixed it" than re-route and fix it.
Either way, you will have learned another great lesson in luthier.
