Plugin update is nice feature, and I use it for some of the plugins, a WordPress SEO - to name one.
Though for other plugins I don't care about updates, because I have significantly modded their source so they would perform how I like them to.
Guess what will happen after the update? All the customization would be lost so I don't want to update it, as long as it works. And if it stops working for some reason than I update it manually. Its not something that we would expect to happen every day.
So I would suggest to add a feature to stop the auto-update for some of the plugins we select.
What do you think?