The issue with Full Annexation is that the Crystal Ponies just got out underneath a tyrant, we need to give them some time and little space to deal with that trauma before we broach the idea of them being a part of the Empire permanently. I know that in many cases it's better to ask for forgiveness than permission, and that it would ultimately be for their own good... but would they recognize that? Some of them, maybe, perhaps even most of them if we're lucky, but there'd always be that minority that whispers we're no better than Sombra, we just had less magic and a bigger army. I want to nip this in the bud now before it becomes a problem later, and let them decide for themselves what they want to do, after we give them some support and help them rebuild of course. Is it more annoying and complicated this way? Undoubtedly, but that doesn't make it any less necessary. Imagine what might have happened if we had strong-armed the other provinces into joining our Empire instead of using diplomacy (painful as it may have been at times), would we be anywhere near as culturally united as we are now?
The issue with Full Independence is that it makes nobody happy. The Crystal Ponies both want and need our support right now, Full Independence would see us abandoning them in their time of need to let them figure shit out for themselves. And I've pointed out several times already just why that's such a terrible, callous idea. We can give the Crystal Ponies greater support and greater aid if we make them a part of our Empire, even if only temporarily. And in the mean time hitching their government to our infrastructure until it can stand on it's own keeps their government from collapsing into corruption and anarchy. Furthermore, it would make our own Citizens grossly unhappy, and for good reason. They fought and they died, and they suffered to save the Crystal Ponies, on our orders no less. Then we took these ponies into our nation at their expense, and encouraged our citizens to welcome them into their homes out of love and compassion. New family units are already forming because of this. By this point our people probably see the Winter War as an extension of the Reunification War, rescuing a beleaguered populace from a terrifying tyrant, and welcoming them into the warm bosom of the Empire of Gryphus. Normally this wouldn't be the case... but, well, we succeeded really well with integrating the Diamond Dogs, and our people don't see this situation as being any different.
So yeah, I'm advocating for a careful, measured approach, because doing this is well worth doing it right. We owe it to the survivors... on both sides of the war, and we owe it to all the people that lost their lives so that we can even have this option in the first place.