By integrating anything shell-based with anything web-based you encounter a plethora of potential exploits and security holes. That said, if you need to run a script that requires command line parameters, and all you have is standard in, then write a wrapper script that reads N lines of text from stdin first, then parses those lines into the parameters you require.

You have to be very conscious of input escaping and validation, though; otherwise your box will be owned in no time.