サ・シャ are from the Chinese morpheme
shā. Usually, when
砂 is read
シャ, it represents the Japanese version of this morpheme.
In this case,
ザ・ジャ, which has a similar sound and meaning. Since the reading isn't quite the same, it's a hint that it might not represent the same morpheme. I decided to search for support for this idea by looking into the etymology of
じゃり. Although I don't have access to 日本国語大辞典 myself, I found a blogger who researched the subject and posted about it:
This seemed to confirm the idea. It appears that
じゃり was originally of Japanese origin, and was spelled with the kanji
砂利 at a later date. Presumably they were chosen because
砂 represented a similar meaning, while
利 together represented a similar sound. Because of this, the reading became an exception.
As for your other question, it appears that both
ざり used to be common, but
じゃり is more common in modern Japanese. Perhaps someone else will be able to be more specific on this point.
(I'm a bit outside my comfort zone on this post, so if anyone has corrections or confirmation to give, I would be most grateful.)