I'm not sure I understand. You're saying miktex is a dependency of pdfcrop.pl? Looking at the source it seems like it should only need ghostscript?
EDIT: I see that it uses pdftex to calculate margins
So why do you want to make a monolothic distribution anyway, Let people who want to use it install MikTeX.
EDIT2: You can compile pdftex as a standalone
http://www.tug.org/applications/pdftex/