Akismet using too much memory and causing 500 error

I installed Akismet comment spam protection earlier today. As there was lots of spam on the site already I clicked the button to check all comments already on the site for spam. This seemed to be working, but after a while I started getting a 500 error when in my admin section. Now I get the internal server error throughout my admin section if Akismet is activated. I've switched debug mode on and can see it's because there's too much memory being used.

I have manually deleted the files, and that sorts the problem. The issue is, when I reinstall the plugin I get the 500 error back again.

How can I stop the process running and start over?