That's a great question and it is a point I was making in my last post --- though I admit it was done only implicitly and could have been made more explicitly and clearly. First though, I would correct the notion that the Desert Abbas and Ammas "left the Church". Rules for participating in the Church in a meaningful way were not developed as they are today and the Gospel of Jesus was unique and recognizable amidst the cultures of the time. The Desert Abbas and Ammas lived a radical Christian discipleship and they did so explicitly; they lived lives of prayer rooted in the Scriptures and praying the prayer of the Church. Beyond this they were knowledgeable about Church happenings and concerns and concerned themselves with these as well. (Remember that Anthony, for instance, assisted his friend Athanasius in his battle against Arius, and Anthony was one hermit associated for parts of his eremitical life, with the deepest of deserts.
Today, hermits are called to participate in Church life in more well-defined ways, but again, there is significant freedom so long as the steps hermits take in their solitude are mutually discerned or discerned under appropriate supervision. Lay, priestly, or consecrated hermits are part of the Church. Consecrated hermits live their lives "in the name of" the Church, and traditionally hermits are spoken of as existing in the heart of the Church. Of course, this must be made real in various ways; one's living ecclesial life cannot be merely nominal. We can't effectively leave the church and cover that over with the label "hermit" or "eremitical solitude" or "eremitical hiddenness". Canon 603 is one way of assuring this too.
But back to your question. Yes, the Church in publishing canon 603, not only protects the eremitical life from isolation, eccentricity, and engulfment by "the world" (by values which contrast with and supplant those of the gospel), but she has brought a prophetic vocation right within her life. She thus assures everyone that folks living lives like those of the Desert Annas and Ammas do so not just within the Church, but in her name as well! Cynics can say she does this to blunt the force or impact of their prophetic quality, but this will not wash. Generally, Hermits today are regarded as incredible or entirely irrelevant. They may be objects of curiosity or interesting matter for a wildlife or psychology journal, but significant lives? Hardly. Had the Church feared the prophetic power of this vocation they could have simply ignored it. Instead she recognizes this life as a vocation and gift of God and composes a canon which defines normative characteristics and makes some instances of it part of the consecrated state! The Church only does this with the things she holds as valuable and even indispensable to her own life.
By the way, this could be said to be another dimension of the way the vocation is ecclesial: it is formally and explicitly (canonically) lived within the Church for the sake of the Church herself! This is an implicit part of the rights and obligations of canonical eremitical life. Thus, those things that protect eremitical life in canon 603 also assures the potential for a vital prophetic presence within the Church --- something which likewise will help to maintain the Church's own prophetic presence in a world so much in need of it.