Fatal error: Allowed memory size with Search Regex plugin

I’m using Search Regex to remove all outbound links from my database, but as there are many (thousands), I always get an error such as:

Fatal error: Allowed memory size of 268435456 bytes exhausted (tried to allocate 71 bytes) in /home/mysite.com/wp-content/plugins/search-regex/searches/post_content.php on line 24

Increasing the memory limit in wp-config.php or php.ini doesn’t work, there is way too much memory consumed it seems.

Is there a way to pause the execution of the script or to break it down in smaller replacements so that I don’t get this error?

http://wordpress.org/plugins/search-regex/