Honestly, this is about the best-case scenario I can see.
The Panacea restores the Emperor to peak physical health. It does nothing for the Psychic/Soul damage He has suffered, still leaving Him functionally as a catatonic body still stuck on the Golden Throne. Except now He doesn't have to spend His power on staying anchored to the Matrium/not dying, so in effect it gives Him more power to work with. And with a better hold in the Materium, more precision, perhaps.
And some of the most important and powerful people in the Imperium have to live with the fact this all is only happening thanks to a heretic.
And on the Beastmen situation... I could totally see this Cane having the GENIUS idea to destabilize his growing realm by giving all the various abhumans and stable mutants equal rights with 'normal' humans. Cane, of course, has no idea just how tolerant and accepting his people have grown living for so long in a society not screaming rampant xenophobia at them 24/7.
So instead of destabilizing, Cain triggers a massive immigration surge and several new rebellions he now has to go 'aid in the Liberation of'. And in the end of it all...
...
"And so we have gathered here today to give praise for the gifts we have received. For generations we have been scorned, dismissed and sent to our deaths for the horrible 'sin' of being born. But no longer! Not here! Here, we walk as free men, with our dignities intact, with the freedom to choose our own path, with the same respect given to us as any other human being. And so, my friends, brothers and sisters, join me in praising that which we are owed this all to. Praise Chaos!"
"Do we really?"
"What? You DARE..."
"I mean, yeah, we have all those things now. And yeah, the Three are around, getting worshipped, by others and some of us here too. But what has Chaos done for us, really?"
"They have given us..."
"Well, no. It wasn't Them that did the giving, were they? We all remember The Speeches smuggled to our world, The Hope they gave us and the unity of purpose for our tribes to rise up and cast down the shackles of our oppressors. The Gods may be there, and they may reward their most fervent followers, but ultimately, I think we all know just who we should give praise to for bringing us here today."
"Huh." "Yeah, now that she says it..." "Fair point, really..." "*Growl* Oh, sorry, I skipped lunch to make it here."
"Well, I can't refute any of those points. And really, now that I think of it... Indeed right you are. So, Everyone! Let us give praise to the truly deserving one, who has brought to us the life and freedom the followers of the False Emperor sought to forever deny us! Praise Cain!"
""Praise Cain!""