try any female college/university... they all have safe female dorms/hostels..
or try the YWCA (which is secure and womens only from what i read on the internet: http://hotels.lonelyplanet.com/pakistan/karachi-r2100312/ywca-p1031789/)
YWCA is the female version of YMCA
Young Women Christian association..
from yahoo answers (copy paste)
Both hostels are being operated by the non-governmental organisations. One, the Young Women Christians Association (YWCA) has its premises in the centre of the city on M.A. Jinnah Road next to the Mama Parsi School and the other one being operated by the Pakistan Federation of Business and Professional Women in Clifton behind the old Mideast Hospital. Both of these hostels admit only those women who come from other parts of the country.
Pakistan Federation of Business & Professional Women's
Dr. S.R.A Women's Complex, Street No.2, Block-9, KDA Scheme No.5, Clifton, Karachi, Pakistan
+92 21 587 3717, +92 21 586 0690, +92 21 537 8064