We could debate, of course, whether historically women's colleges are a good idea at all. The strongest justification, I think, is one the article mentions: women's colleges let women go to school in an environment where every leader--the student body president, the editor of the college paper, the star chemistry student, the best hip-hop dancer, everyone--is a woman.
We grow up knowing in an abstract sense that women can be these things. But abstract knowledge is different from four concrete, formative years spent seeing and experiencing women filling all these different roles. This argument makes intuitive sense to me, but I have no position on whether it's valid; I honestly don't know where I stand. But let us assume, for a moment, that the argument is right, and that seeing women fill the full panoply of roles at college does offer women a transformative experience that broadens their outlook and sense of their own possibilities.
If women's colleges are a good idea, then it makes sense that they should include people who identify (solely?) as women, and exclude people who do not. This excludes people who identify as men, trans men, people who identify as neither women nor as men, and people who identify as both women and men. (Note that this definition does not exclude trans women; it makes perfect sense to me that trans women should be able to attend women's colleges, but I suppose that is another argument for another time.)
One of the trans men in the article explained his attendance to attend a women's college as a logical part of his identity struggle. He figured he'd see all kinds of ways to be a woman at an all-women's college, which might let him embrace the gender he was assigned at birth (female). But encountering these different iterations of woman-ness actually convinced him of the opposite: no matter how he chose to "be a woman," it didn't feel right. He ended up coming out as a trans man.
This guy's experience makes sense to me. He wasn't looking to "infiltrate" an all-women's college; he was looking for a way to be himself. But he discovered that any way he looked at it, his "self" was a man. People usually attend college from ages 18-22 in the United States, which often coincides with self-discovery and identity-related realizations. It's only natural that in the 21st century, some people will come out as trans--and it's crucial for them to be in a supportive environment when they do.
Now comes the "but" part.
But... if we do believe that all-women's colleges are a good idea, I don't think you get to attend one if you don't ID as a woman. I think you should be allowed to finish out the academic year there, including starting to physically transition, hold leadership positions, etc. if you want to. Disrupting college during an academic year is seriously tough, and seems unfair.
Then the college should completely hold your hand throughout the transfer process to a similarly reputable institution, with similar financial aid, that meets your academic needs. But I don't think you get to keep going to, say, Wellesley, for three more years while you grow a beard, take a guys' name, and run for student body president. That's just not fair to your hundreds of peers who came to a women's college to see women holding every role in the place. And a trans man, of all people, should understand this--presumably at the outset, he selected a women's college for similar reasons.
There are great ways colleges can handle this. It needn't be a case of "kicking out" people who take T, say. A trans man's acceptance of his identity as a man should be respected and celebrated. The school's attitude should be, "Awesome! We're so happy for you and will support you in every way possible, including excellent counseling and medical care. And part of supporting your identity means finding you the absolute right place to continue your academic career as a man."
To me, the answer really lies in what we see as the point of an all-women's college. Is the point that women see people who were born with vaginas living out all kinds of different lives? If so, then trans women should be excluded and trans man should be included. Is the point that women see traditionally "feminine" people in all kinds of different roles? If so, then trans men and butches should both be excluded. But as I understand it, the point is really for women to be in an environment wholly comprising other people who identify as women. To me, the validity of this goal is the question we should really be debating. If we believe that it's valid and important, doesn't the rest kind of follow?