Federations and organizing committees have exactly zero say in who gets a visa. And why should governments care and make exceptions for skaters? In contrast to the ban by the ISU, the sanctions by the different governments aren't just supposed to hit anyone representing Russia in any official capacity, but all people with (solely) Russian citizenship/Russian residents. (In the hope of destabilising Russian economy and animating Russians to rebel against their political leaders)
And the issues skaters with only Russian citizenship but representing other countries might face are completely independent of whether or not Russia and Belarus are banned - Nothing would be any different if Russia and Belarus could still compete internationally. Except that you'd have a lot more skaters struggling to obtain visas.
And by the way, if you're not aware of this, the ISU has indeed gone out of its way and moved some skaters with (potential) visa issues to different GP assignments (something I don't remember the ISU ever doing). There's really not much else they can do.