This Bible passage was my first encounter with anti-Catholicism and it bothered me because as a convert I had never thought much about the Blessed Mother...sort of like how I was when I was a Protestant. Now at the time this happened I prayed very hard for an answer to the question, "Why would the Catholic Church lie?" It took a few minutes but, part the answer came very quickly. To my immediate request in knowing why the Church had lied I was given a bit of grace to understand that indeed it doesn't matter whether you are referring to Christ in this passage as He shall crush or strike...or to God's mother as "she" shall crush or strike. Jesus came into the world when the Blessed Mother said "be it done to me..." So, in this sense she did "crush" the serpant's head, through her Son, a.k.a. God.
I looked this passage up in three Catholic Bibles:
Douay-Rhiems translates as you said, "He shall crush..."
New American Bible St. Joseph Ed. translates "He will strike..." and
Monsignor Ronald Knox translation "She is to crush..."
I looked then to the notes in the Knox translation and this is what he had to say about it:
For "she" and "her" the Septuagint Greek has "he" and "him"; the Hebrew text also, as it has come down to us, gives "he", or perhaps "it". But most manuscripts of the Latin version have "she", which plainly gives a better balance to the sentence. That the reference of this passage, in any case, is to the Incarnation, is the general opinion of the Fathers.
I have seen the passage translated in at least one other Catholic Bible as "she," sorry I do not remember which one it is, perhaps the Revised Standard. In any case the experience led to further interest in what the Church Fathers had to say about the Blessed Mother. I have a great devotion to her now. I have heard it said that Marion devotion is one of the last things most converts accept.
I agree the passage works both ways He or she. But I think that passage has a future as it were. I think there is more to come, if for no other reason than Satan has not been crushed just yet. Mary is the prototype Christian and we are called to be in union with Christ. The Latin Mass makes this very clear.