One of the great things about Shakespeare's plays is that they're rich enough to leave lots of room for interpretation. This interpretation is not one that I believe is the most obvious or finds a great deal of support in the text. Shakespeare rarely wrote in such a cut-and-dry fashion, neatly matching characters to values or real-life people. Instead, he often writes multi-dimensional characters that can be seen in lots of different ways, or borrows from older traditions of stock characters, like the Fool. While Measure for Measure is heavy on stock characters and archetypes, they don't correspond allegorically the way that, say, characters in Pilgrim's Progressdo. Isabella, for example, who would be reduced to a symbol for the Church--but which church? The Catholic Church? If so, thanks to England's fraught history of the Reformation and Counter-Reformation, you've got a complex situation on your hands--far more complex than that summary where she is the salvation of the corrupt state suggests.
There are lots of other interpretations that make more sense to me. For example, Victorian women writers like Anna Jameson and Mary Cowden Clarke were inclined to see Isabella as a woman whose defining feature was her emphasis on prizing virginity. Not all writers agreed whether this was good or bad, or whether virginity should be a virtue prized above the protection of her brother's life, but they didn't see her as an emblem of any church.