Yes, any app that you have installed will be gone after a factory reset. It will restore your rom to the state it was in upon flashing.
You can make an update.zip of Titanium in the settings and flash it via your custom recovery to re-install it, or you can re-install it from the Play Store.
Also, as long as you aren't wiping your internal storage/sd card, a factory reset via your custom recovery should not wipe out any of the backups you have made; it will just remove the app.