I personallly would still breed her then bc it only effects them "sometimes" and its a female so it will be only one clutch at a time compared to a male with the defect breeding multiple females. Couldnt you just feed off the sickly babies when they pop up once in awhile right away? or would megacolon be bad for your snake?
EDIT: After looking at some of the pics in that link i think breeding the off eyed rat would definetly be ok. In the "4 week old" rat picture it shows that huge bulge in its side. If i saw that i would feed it off right away, as soon as i noticed it. Idk why someone would let it live in pain like that for 4 weeks...