it's not such a bad idea- as long as you use a permenent ink marker- people use markers to highlight- and change things on quilts all the time-
if the white thread showing bothers you go ahead and (paint it)
one thing though- i have found most of the time when the sid is not quite right---once the quilt is washed and dried you don't see that anyway-
but the marker idea is not being lazy- or a bad idea- it is a 'normal' fix by many quilters.