First of all, I would disagree that "most" (meaning to me more than 50%) women runners burn out in their 2nd year - Womens running at the college level has never been deeper or better and continues to see great progress.
However, I can see how it might seem that way.
The attrition rate for college runners (M and F)in general is pretty steep. For a lot of reasons many runners figure out early on its just not worth the sacrifice. Most on the edge can stick it out through frosh year but by the next year are more comforatble in their surroundings and leaving the team is not as much of a sacrifice. So I would agree if you are going to quit that probably is when most do it.
Add in that most women, unlike men, have their biomechanics significantly altered by maturity and require significant time and effort to adjust. Some never do or are just not the runner they once were. Some figure its not worth the effort to start over and quit. This is worse for prize recruits, who were so far in front of everyone in HS but may significantly regress before they can again handle the training necessary to compete at a high level. This also opens up the opportunity for runners who were untrained or come out of puberty with good biomechanics to rapidly catch up and pass girls they were well behind in HS.
Finally, in proportion to the number of quality runners in HS and college there are a lot more spots on womens teams for college runners then there are for men. This means more fringe runners on rosters and more fringe runners means more drop outs.