I can't say I've ever basted a whole quilt together before sewing, but I've often basted in order to hold things together while sewing a shorter stitch. There's a perverse kind of pleasure in ripping out the basting threads because they bunch up the piece so it looks a mess, then - pop! - out they come and the piece goes back to flat. I can understand it would be difficult to remove the basting threads if you've sewed right over top of them since the stitching would hold them in. Those threads should cause no trouble for you; at worst they will work loose and need to be snipped occasionally. If this was my quilt top, I'd leave the basting stitches in unless they are causing puckering.