This is a topic I've been reluctant to discuss, mostly because I don't like to make an issue of something that should really be a non-issue. I think Justine Siegal, who got a lot of press for being the first woman to throw live batting practice to a major-league baseball team, proves why the whole thing should be a non-issue. As the first base coach for the Brockton Rox, she seems a consummate professional and the players seem to respect her, so it really shouldn't matter that she is not a man. It's the same reason why I have never made a big deal out of being a female blogger. I don't like to get into personal stuff anyway, and I prefer my work to stand on its own merits; I certainly don't want my gender or what I look like to serve as a distraction.
I don't really know if women are being actively discriminated against when it comes to finding jobs in major league baseball. No woman has ever served as a general manager, and few women have ever held positions in baseball operations, but with no data readily available on the pool of qualified candidates, it's impossible to say whether women are being kept out or if they simply aren't interested in these jobs. That isn't to say that discrimination doesn't exist in major league baseball (it is pretty well-documented in other traditionally male-dominated fields, after all), there just isn't any tangible evidence of it. Anectodal evidence isn't really good evidence at all, but for what it's worth, I don't know many women who have the background necessary to work in a front office. Though I know many women who are passionate baseball fans, I am one of very few who is interested in sabermetrics. Most of the female fans that I know follow baseball because it's fun, and that's fine; not everyone has to be a nerd like me. But to compete against the thousands of qualified male applicants, a woman has to know more than the difference between a single and a double.
The argument that the players would not respect a female GM because she has never played professional baseball is bunk; only three general managers working in baseball right now have ever played the game professionally. The game has changed a lot in the past ten years, and the emphasis on sabermetrics means that front offices are increasingly being staffed with executives who hold advanced degrees in economics, finance, and mathematics. There is no real good reason why a woman couldn't be one of them.
If there is going to be any place for women in major league baseball, it will have to be in the front office. I don't think women can, or should, play baseball alongside men. Women just are not physically as strong or as fast as men, and it's difficult to imagine any woman actually making any major-league roster. It's not the politically correct view, but hey, fact is fact, unswayed by popular flights of fancy that women are exactly the same as men in every single way.
That doesn't mean that girls shouldn't play baseball; it would actually benefit the sport to have more knowledgeable and passionate fans, and there is no better way to do that than to have separate girls' baseball teams (I wished I could have played baseball when I was a little girl; I hated softball). The notion that women aren't athletic and can't play sports is patently false; they may not be as fast, or as tall, or as strong as men, but they can certainly play at an elite level against each other. Women could probably excel at baseball, since they wouldn't have to compensate for a lack of height or physical strength by altering some of the fundamental aspects of the game, like they do with basketball. They wouldn't be able to throw hard enough or develop enough power to succeed in the majors, but they should do well against other players of a similar skill level.