As I read mandog's description, I see the SQLite data store being used as a simple, asynchronous transfer mechanism for getting user input from the PHP to the Perl. Clearly, the Perl side needs to Do Things To The Data along the lines of untainting it (in effect), as the data in SQLite is unfiltered.

Base 64 encoding should be a portable scheme for encoding in PHP and decoding in Perl for closer examination. Once it is encoded, there will be only printable characters, and none of them will be single-quotes. Thus, running it through sqlite_escape_string will not do anything to the string.