If specific sounds in Kazakh disappear because "they were written the same", it merely means that the particular sound distinction was already being phased out in the spoken language. If the sound distinction is gone, separate symbols won't save them. It will merely become yet another opaque spelling rule for children to memorize.
English "th" represents two different sounds, and English speakers manage just fine, because in its sound system they are totally distinct and never confused with each other.