GIMP :: Paint / Fill Antialiased Areas Of PNG?

I've used GIMP to great effect for quite a while now but I know I'm taking the long way around on a lot of things because I'm not very savvy on CG stuff, so I thought I'd ask here. I actually was registered with Gimptalk but it appears to be gone? Anyway...

I am currently making my own 'original artwork' by using usually open source/public domain photos and such, and using transparent layers to "draw" lines over them, making my own lineart. My problem is that I can't seen to find a "turn antialising off" checkbox in GIMP.

Even if I did, I do some postprocessing in Inkscape to turn the lineart into something more smooth, and then it re-antialiases (is that even a word) the picture, and when I try to use the paintbucket to fill in the lineart to get simple color pictures, I get lots of white specks and dots from the antialiased edges of the smooth lines.

What do I need to do to a picture to make sure I can fill spaces with a color right up to the lines, AFTER it has been antialiased, in my example? I can't use duotone or index to 2bit color or whatever, because that bites chunks out of the black lines and also destroys the smoothness of the Inkscape processing, but even if I haven't used that, it still reduces the lines spottily.

I've tried turning the tolerance way up and filling the areas with white first, hoping the white and the near-white specks will be close enough to "bleed" together so I have one color, and then paint with the desired color, but it still has specks.

Also, how to do lineart to achieve the same results I'm trying to achieve. I'm hand-tracing over the lines by eye, which, though I'm good at it and it doesn't take long, is more time consuming than it probably should be, and tedious.