Quick note: I'm not an artist.
Simple solution, don't add lineart around your character. Think in terms of vector, if you don't add a black line around your character then scaling up & down will be less of a problem as it will be harder to notice the artifacts. You could consider using a more subtler color for the lineart, by trying a slightly different shade of color based on what color is currently at the side of the line you are drawing.
Because VS doesn't have vector support, there's not a right lot you can do about scaling issues. Daedalic have created over 10 games with Visionaire Studio now & the scaling artifacts don't seem to bother them - at least I've not heard anyone mention them complaining about it.
My advice would be to try & draw the character at the size you want the character to be at 100% scale value. Maybe you could consider creating height chart for your characters that you draw on paper? If you can work out how tall your protagonist is, then you can figure out the correct height you need to make the rest of your characters.