I previously discovered the hard way that it's not a good idea to simply delete the plugin folder without uninstalling. If you do that, you won't completely remove it (which can create conflicts with other plugins) and won't be able to reinstall.
If you're having problems with internal server errors, what you might try is accessing the site via FTP or shell, downloading the wp-config.php file, and looking for this line:
define( 'BWPS_FILECHECK', true );
Comment this out (adding two slashes in front of it should do the trick) and upload the edited file in place of your existing wp-config.php. This will disable the file checking system.
If that allows you to log in again (it did for me), go into the Security options and uncheck the box for "Enable File Change Detection." (If you comment out the line in wp-config, the plugin may still think the feature is enabled even though it's not.) That will stop the file checking.
At that point, if you want to get rid of BWPS, you can deactivate and uninstall it. You could also leave file checking turned off and get a different plugin to monitor file changes. I guess BWPS' file checker is load-heavy, which can be a problem on shared servers.