If not binding is about 6mm and it looks like you should hide most if not all of it, could also skim the back down a little to make sure. As for filling I'm a fan of superglue and sawdust. 

But yeh, turn it over and carve that out would be my thing unless the other side looks amazingly good? 

All like while ago I bought a carve top that has inclusions/ bark holes in the side I want to use as the glue side. I knew it was imperfect when I bought it.

What I'm wondering is it I should I use something to fill the holes before I get to the point of gluing it to the body? I was thinking stabilise with thin super glue and then just fill with wood filler?

I was planning on binding the body too.

I've marked the offending area in the attached photos. The pencil line in A is roughly the edge of the body and shows the intended underside/glue  side of the top.

B is a close up of the area in photo A. C is it from the side after I'd taken some of the excess off the sides and D shows the area from the intended carve side.

 Cheers! 

Dan