In Vivado Design Suite 2012.3, there will be a -bin_file switch to write_bitstream to generate bin files. Currently, there is an issue in the way the bin file is implemented in native bitstream that is to be fixed in the 2012.3 release.
To work around this problem, use the -ise switch and rely on the ISE bitgen flow.
Example Template:
write_bitstream -force -ise -bitgen_options {-g binary:Yes} output_file.bit
The -ise switch will no longer be needed in the 2012.3 release.