I've heard good things about Phrozn. http://www.phrozn.info/en/
First things first, how is a flat file setup slower than running from a database? There is absolutely nothing deployed but flat files.
Secondly, one of the big advantages of using something like Jekyll is that your entire site can be put into source control and deployed, backed up, and moved around with complete ease. It can also go on any server, regardless of setup. You can chuck SQLite into source control, but what is the point if you just want flat files? It'll be faster to serve files instead of an embedded db.