This was bugging me as well. I was able to tweak the plugin to change this manually. It was easy enough. Just do a find and replace of all instances of wp_get_shortlink with get_permalink.
I found five that needed to be replaced:
Search "wp_get_shortlink" (5 hits in 3 files)
\wp-content\plugins\social\lib\social\controller\aggregation.php (1 hits)
Line 38: $url = wp_get_shortlink($post->ID);
\wp-content\plugins\social\lib\social\service.php (2 hits)
Line 386: $url = wp_get_shortlink($post->ID);
Line 462: $url = wp_get_shortlink($comment->comment_post_ID);
\wp-content\plugins\social\social.php (2 hits)
Line 140: $url = wp_get_shortlink($post->ID);
Line 1121: $shortlink = wp_get_shortlink($post_id);
There were also two instances in the README.txt file but those can be ignored.
The only problem is when you do this it will truncate the other content in your Tweet, e.g. https://twitter.com/SeattleBubble/status/257904154129874944