Why not just use an existing program such as Genepop and write your own script to generate input files? Genepop provides plenty of example input files and once you have input your data it runs very fast.

Because Fst calculations are so much less complicated than iHS, we take a very programmatic approach to Fst calculations for our SNP panels. We have written a program to do this in a high-throughput manner. My colleague wrote a script in R or Perl, but this is so simple that it could even be done in Excel.

The R package hierfstat can do this. As well as computing Fst values, it can group your populations and compute Fst values for the groups. Very flexible. For in the input file I think plink ped files may need some reworking as it's been sometime since I've used it but the vignette can help you with that. Also has some cool functions for generating sample SNP data to vary mutation and migration rates and things like that.

Documentation here: http://cran.r-project.org/web/packages/hierfstat/hierfstat.pdf