I have a php script written which calls an external command using exec which compiles a spacial database query result into a shape file. In tables with lots of records (say
Premature end of script headers means that webserver's timeout for CGI scripts was exceeded by your script. This is a webserver timeout and it has nothing to do with php.ini configuration. You need to look at your CGI handler configuration to increase time allowed for CGI scripts to run.
E.g. if you are using mod_fastcgi you may want to specify the following option in your Apache config: FastCgiServer -idle-timeout 600
which will give you timeout of 10 minutes. By default fastcgi provides 30 seconds. You could find some other fastcgi options here http://www.fastcgi.com/mod_fastcgi/docs/mod_fastcgi.html