Sqlite from what I have read up on is a very robust db that can hold over 1 TB of data. Most of the problems of corruption are due to something else. As I see it you have 2 options.

1) Back up the directory, wipe and re-install to see if that fixes it, if so its the db.

2) If the problem still exists, look for other issues, disk space, memory issues, etc.

It sounds like you are self hosting on a personal server, I would go with MySql if you have to re-install. I had degrading performance (just getting slower, still worked good) with about 40 feeds and 40k of items.

Maybe someone else has better options, you could save a copy of your config file so you don't start from scratch. Also it is easier to backup the feed list from MySql.