I'm afraid that the word "they" is not a proper singular gender-neutral pronoun.
You're right, it isn't. But it provides a better alternative than using masculine or feminine, which constrains individuals to two genders. And it is also more preferable to lesser known gender-neutral pronouns, such as zie/zim/zir, as that will lead to confusion.
This has been an ongoing discussion on my college campus for the past year, and from conversations with individuals in our Office of Multicultural Affairs, including those most affected by this, I believe this is the proper way to proceed.