If a person is accustomed to only distribute his ma’aser money to the poor or for the support Torah scholars, this would not be a permitted allocation.
However, Chafetz Chaim writes that if at the time a person takes on the custom of ma’aser he stipulates that he reserves the right to distribute it according to his discretion, he may then use his money to voluntarily support other worthy causes. Thus, if you have always been accustomed to distribute your ma’aser for mitzvot like the beautification of a shul or the publication of Torah books, you would likewise be entitled to buy the mezuzot from your ma’aser money to ensure that the mitzvah will be fulfilled and that your sister will be protected spiritually. This is true especially in your case since you say that would not be able to do the mitzvah without using ma’aser funds.
Incidentally, this allowance would not be limited to your sister. You could also use ma’aser money to help poor or unaffiliated Jews fulfill this mitzvah or others.
One note of caution: I would suggest that you discuss the matter with your sister beforehand to get her permission. You don’t want to appear as if you are pushing your religiosity onto her and her family. Handled correctly, your concern and kindness may inspire your sister to greater Torah observance, in general.
 Ahavas Chesed 2:18.
 Ibid. 2:18 n.; Agur B’ohalecha 2:55.