The problem seems to be there aren't always enough resources available for Perl to read this into memory. Instead of dealing with that whole chunk of data as a scalar, I would want CGI to save it to disc somewhere and just point me to the file.

To me that is a different problem than a Perl issue. Almost sounds systemic to me. If, for example, you are running this code on a system with 4Gb of RAM (pretty common these days) and you are running out of memory then you need to constrain the data to be in smaller chunks.