anyone? 

I think your best bet is to just use the ApplicationDbContext<SiteUser> directly, like so:

using (var userDbContext = new ApplicationDbContext<SiteUser>(connectionString))
{
    var user = userDbContext.Users.FirstOrDefault(x => x.Email == email);
}

And if you want to use exactly that instance in any other dependency during your job, you could create a nested container for your job, like so:

using (var container = _container.GetNestedContainer())
{
    using (var userDbContext = new ApplicationDbContext<SiteUser>(connectionString))
    {
        container.Inject(userDbContext);
        var dependency = container.GetInstance<IDependency>();
        dependency.DoStuff();
    }
}

The inject method replaces any existing instance of the provided type, and more importantly - it tells StructureMap not to use your regular ApplicationDbContext<SiteUser> which was probably registered using () => HttpContext.Current.GetOwinContext().Get<ApplicationUserManager<SiteUser>>.

The nested container disposes all its created objects at the end of the using statement, so using a nested container is probably a good idea in any case. It defines a obvious lifecycle for your dependencies.

This also means, of course, that you move your dependencies from the constructor (which only needs a IContainer) to resolving them via the nested container.