Should I change "index" to "indexes", and thus "was" to "were", and "that of" to "those of"?
That doesn't really get rid of the ambiguity, it just changes it to a different ambiguity.
A reduplication of the preposition can help here to make explicit how many there really are.
In urban areas, the graduation index of (or for) general high school
and [of or for] higher education [was?] were greater than one, while
that of (or for) compulsory education and [of or for] secondary
vocational education [was?] were smaller than one.
This may be the best way to get the one-index-per-item-listed point across.
The changes you suggested may imply that there are multiple graduation indices associated with each one. Perhaps context handles this problem, but as a stand alone statement, English is severely challenged when trying to handle the distribution of a plural subject across multiple PPs. Grammar doesn't handle this. If you want to be precise, you just have to explain it in words.