What a small small world this is! Last month I needed to do something similar using
ProFit. I didn't see the need to wrap the program with Perl though, since it's a command line application that supports scripting (you can pass your profit script using the -f flag).
So, to align an arbitrary number of structures, I created a text file that only said "fit", and then I looped using bash:
for F in *.pdb; do profit -f script.txt complex.1.pdb $F \\
>> output.txt; done
Then I used grep to just keep the RMSD value of the run for each structure:
cat output.txt | grep 'RMS' | awk '{print $2}' > rmsd.txt
Of course, for anything slightly more complicated than that, I see why you'll want to use Perl.
If you think it's worth it, consider writing a module under Bio::Tools::Run, so that you can later share your wrapper with everyone. You should look at the Bio::Tools::WrapperBase module and subclass from it; it'll give you a nice interface with all the error checking built in. I could help you do it if you want to!