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The GUI updater is part of PackageKit, and since Fedora 21 is mostly independent from yum (and yum's replacement, dnf).

PackageKit ignores exclude directives in /etc/yum.conf but it does still obey them in the /etc/yum.repos.d/*.repo files defining the package repositories, so you can add exclude=foo bar bz to /etc/yum.repos.d/fedora.repo and /etc/yum.repos.d/fedora-updates.repo to prevent PackageKit from trying to install/update those packages.