It would not make federations the same as alliances. A member still would be unable to withdraw without inviting war. How does it make any sense that one realm abusing its federation can only be dealt with by the entire federation declaring war on one another?
They can always send troops as murderous. Or all break the federation, and re-ally each other but declare war on that last guy.
It's ugly and not as quick, but it can be done via other means.