It hasn't been removed, it has been limited to obit use in all Nations other than NI, who also use it for programmes 'of National reflection'.
Let's not get too pedantic. The number of playouts per year doesn't make it into double figures. And apart from NI, I've not heard of it being played in any of the other nations in recent years. That's as good as removed in my book. Do we know when it was last used on network?
The only thing to consider is the Circle swirl has to form up over the end shot, some 16" in. They can't place the swirl any sooner as it would completely obscure four people's faces. While they sacrificed this with the very fleeting shot of the man on the balcony with the long edit of Capes, I don't think they would find four obscured faces, and also those faces being close to the camera, as acceptable.
If they insisted they had to have the logo form-up appearing after a few seconds, then yes, using the original version would be a problem. However, a short version of this could've been created, using a couple of the pre-form-up shots from the original edit and then have the logo form up over the moon shot. Although the music would probably need adjusted too. There's no excuse for taking this ident almost completely out of circulation though. Unnecessarily wasteful.
Personally, I don't agree with the massacring of these idents that occurred in 2009. And with respect to the small number of long versions that were retained, having the logo form up so far in advance of the circle formation in the accompanying video just looks daft. I've only suggested an edited version of Moon as a means of keeping it on air - if it had to align with the format of the other ident edits. However, Moon and its accompanying soundtrack are best left unedited.