This seems like something that should be an option. I'm sure some users would find it extremely annoying, I'd be happy for it to be the default behaviour, though. I realise that this would bump up the complexity of the coding significantly, so @DasSkelett, if you'd like some help with that, just say so and I'm sure someone would be happy to make a PR to your branch to handle the option-setting.

Thanks for your thoughts.
I started to add an checkbox in the settings GUI, I think I can handle it myself, but it wouldn't be bad if someone reviews the code after that.

So should it be opt-in or opt-out?

Make it opt-out.

Okay, I added the option in the Settings menu in a "more Settings" group box:

I think this is ready-to-merge

Okay, don't know why my upstream pull (only containing a495f43) failed CI...

It failed and travis posted something about tcp errors so I restarted the job and it passed... sounds like a network issue more than a codeissue.

Ah thanks :D

Could you move the "Hide Epochs" button into the new "More Settings" group box? It doesn't really belong in Updates.

Moved it, now looking like this:

One more question:
Why are most controls of the AutoUpdateGroupBox depending on AutoUpdate.CanUpdate?
Can't we just block the InstallUpdateButton, if we can't overwrite the exe?
So instead:

private void InstallUpdateButton_Click(object sender, EventArgs e)
{
    if(AutoUpdate.CanUpdate)
    {
        Hide();
        Main.Instance.UpdateCKAN();
    }
    else
    {
        GUI.user.RaiseError("Can't autoupdate. Please check https://github.com/KSP-CKAN/CKAN/ for help!")
    }
}

This would solve the annoying Designer Error in VisualStudio and the Settings window would look nicer if AutoUpdate isn't available.

Edit: I created a new branch on my fork for my question.
Check this commit for my proposed changes.

DasSkellet, can you raise a new PR for the change in controls dependency? I'm not sure what designer error you are getting, as I don't use VisualStudio most of the time.