For Jerome, it was a dilemma. He probably consulted a rabbi, who said: Of course it is the Jewish nation battling Satan. Jerome, being Christian, recognized that not only by grammar but in truth it is Jesus crushing the serpent. However, he probably felt that to translate "He will crush" would be seen as reaching by non-Christians, who can also consult a rabbi.
Something similar is occurring with Isaiah's "virgin shall conceive", where Christians see a prophecy and Jews see nothing out of the ordinary, a young girl, העלמה, getting naturally pregnant. In that case Jerome threw caution to the wind and translated as the Holy Ghost lead him.
Why Jerome followed a judaized interpretation in the case of Genesis 3:15, but not in Isaiah 7:14 I don't know. It could be that to him Mary was a natural amalgamation of the Jewish nation and the Christian Church personified all at once, so he felt a marian reference would resolve the puzzle.
Of course, this is pure play of imagination on my part. It could be that quite simply the copy Jerome was working on had a feminine pronoun.