This isn't really an answer, but I wanted to share that your original usage of exec is actually working for me. This was how I set it up.
data.txt
"1,2,3,4,5,6,7,8"
sort.rb (I don't know what your sort did so I am just writing the same data out)
File.open(ARGV[0]){|f| puts f.read}
irb session
irb(main):001:0> exec "sort data.txt > data.sort"
When I ran this in irb, I did get a data.sort output file and it contained "1,2,3,4,5,6,7,8" as expected. I can run the same exec line through irb or from another ruby file, and I get the output file with data each time.
I am running Ruby 1.8.6 on a 32bit Windows XP system.