I think it's very reasonable to add a checkbox to allow auto-updating Alfred. Right now, my alfred setup is mature, and outside major releases, I don't see any reason to change it. Between several computers, I find myself having to press "update" and then "download and restart" more often than I'd like.
Note also that when I invoke alfred, I was trying to do something. Even if it's not so frequent, it feels frustrating to have to manually intervene to get rid of the notice.