Freelinking does not scale well

I currently use Freelinking extensively on several production sites.

I've started to notice that these fill break when the number of nodes processed by Freelinking gets large.

Symptoms are crashed site with one of the following messages:

• Fatal error: Allowed memory size of X bytes exhausted (tried to allocate Y bytes) …
• Fatal error: Maximum execution time of 30 seconds exceeded

Problem is clearly caused by Freelinking, as disabling the module fixes it.