Well, the nun was well intentioned but sadly misinformed.  

I would argue that God could understand a Catholic becoming a Protestant, an atheist, a Muslim, Jew, Buddhist, etc. What God cannot understand is people who claim to be "Catholic" yet do not believe and profess the Catholic Faith--not to mention are actively dissident.  In other words--people who claim to be Catholic yet want the Church to become Protestant or otherwise preach, teach and profess a liberal, secular, humanist, atheistic Gospel.