Yes, ぢ and じ sound the same. But, look at English-- we use different letters to represent the same sounds, for example mm or mn for the "m" sound. Why not replace "x" with "ks" and "z?" We hardly ever use "x" anyway. We haven't changed our language to get rid of redundancy, so why would Japanese?
Also, retaining ぢ reflects the etymology of the word. For example, when a compound word is made that has a second word beginning with a voiceless consonant, the voiceless consonant becomes voiced. For example, "neko" + "shita" becomes "nekojita." If you do this with with a "chi" word, you'll want to retain "ぢ," not replace it with "じ."
ゑ and ゐ fell out of use because the Japanese language changed in such a way that these sounds were lost. The sound of "ぢ," however, has not been lost, so there is no reason to think that the mechanism that removed ゑ and ゐ will remove "ぢ."
I don't think "ぢ" will disappear until the sound disappears from the language-- and I don't see that happening any time soon. In fact, I think that it's more likely that じ will lose its affrication and become a sound distinct from "ぢ". (You realize that the voiced equivalent of "shi" would not be a "ji" sound, but a voiced alveolar fricative, which is the sound you hear in the "s" of "casual" or the "z" of "azure.")