I have a fucked up theory, but based on Cobra's reaction at the end of the chapter i get the feeling that Imu may have taken over Queen Lily's body.
We are told that the 19 founding Kingdoms of the World Government all went to Mary Goise to become Celestial Dragons, with the exception of the royal family of Alabasta, who at its founding- just so happens to be the reign of Queen Liliy.
Both Doffy and Corba confirmed this chapter that the monarchs who founded the World Government went to become Celestial Dragons and go live up in Mary Geoise, while the royal families in their home countries were replaced, the Nefeltari Family of Arabasta being the sole exception, as said by Doflamingo in Dressrosa.
In Robin's flashback, Professor Clover also stated that the World Government was formed after wiping out the Ancient Kingdom and having its name erased from history.
HERE'S MY THEORY:
The Ancient Kingdom was the previous most powerful Kingdom/Organization, similar to the WG in the current time and had possession of the Ancient Weapons. After its defeat by the alliance of Kingdoms - Imu and his people snatched power in a power vacuum and formed the World Government as the new rulers of the world, and as the new most powerful entity. To ensure their absolute grip on power- they coerced the 20 allied kingdoms to have their royal families and monarchs to move to Mary Guise and replaced them with other families.
This is done to:
(1) take away their sovereignty and independence. If the 19 powerful royal families were taken from their kingdoms - then the kingdoms themselves would weaken due to the loss of strong leadership and effective governance that made them strong in the first place, i.e strong willed and kind rulers like King Cobra. Isn't it strange how these 19 Kingdoms were able to come together and take down the Ancient Kingdom - but in the present time can't even deal with pirates?
(2) the second reason is to keep up the guise that the kingdoms who joined the World Government still have sovereignty, independence and most importantly REPRESENTATION within the World Government because their monarchs became world nobles and Celestial Dragons. When in reality, through time - most Celestial Dragons have been reduced to nothing but mindless fat fools, with the two exceptions of Nefertari Family (because they never joined), and the Don Quixote Family (because by some miracle Doffy parents were still able to remain decent beings even though they were incredibly naive by the real world outside.)
WHAT MAKES ME SUSPECT THAT IMU TOOK OVER QUEEN LILY'S BODY
Now going back to why i think Queen Liliy was murdered and her body was overtaken by Imu and the reason for it. Cobra's reaction to the 5 Elders saying that Queen Liliy is right there when Cobra asked what happened to Queen Lily showed surprised. It could just be his first time seeing someone sitting on the empty throne - but why did Imu bother showing his face at all if he is to remain secret to the rest of the world? Imu's silhouette is short and slim with long gowns - it doesn't look like something a King, or a male royalty would wear, more like a petite female or a Queen. Also, when Imu was looking at faces back in the Pangea Castle, why did he have Vivi's photo when she's not a D, unlike Luffy and Blackbeard? she's the odd one out in that group. I suspect that it's because since Lily is Vivi's ancestor, Imu wanted to see if Queen Lily's face, whom he has taken the body over still resembles her, and Vivi is the closest real-life resemblance. Which makes me think if taking all the royalty photos at the beginning of the Reverie was all on purpose.
WHY DID IMU DO IT TO QUEEN LILY SPECFICALLY?
The easy answer would be Queen Lily never wanted to join the WG and become a Celestial Dragon in the first place. The more important answer could be she learned the truth about the WG real intentions before joining and wanted to refuse. The WG couldn't have that happen, so they murdered her and planned to have fake Queen Lily -Imu sign the papers have him make Alabasta join the W.G in her place. Of course, that didn't happen, and the 5 Elders called the Nefeltari Family traitors, why?
PLUTON.
I believe the answer could be Pluton. Since in the Alabasta Arc, Crocodile suspected that Pluton was hidden in Alabasta, later confirmed by Robin. With Poseidon later revealed to be Shirahoshi in the Fishman Island Arc, it might be the case that the ancient weapons can only be used and activated by someone of royal blood of the families to which the Ancient Weapons lied in. This might explain the World Government's repression of Fishman Island and Ryguyu Kingdom and the Five Elders reason of wanting to erase Alabasta Kingdom. They don't want anybody else having the chance to matching their power- which might also mean the W.G is in possession of an Ancient Weapon themselves. As to Imu taking over Liliy's body - he might need to do it to be able to use Pluton, since the Nefeltari family never joined them - they became traitors of depriving them access to Pluton. But since it was later revealed that Pluton was actually in Wano and not Alabasta, Imu's and the W.G efforts might have been in vain anyway. But Imu does not know that since he can't read Ponyglyphs (otherwise the W.G wouldn't be hellbent on still getting Robin) and still believes that Pluton is in Alabasta and not in Wano, unless there is something else, they secretly know that nobody else does.
TLDR:
King Cobra is surprised to see Imu have the face of Queen Lily. Imu murdered and took over Queen Lily's body to be able to control Pluton one of the Ancient Weapons that Joyboy hid away after the fall of the Ancient Kingdom. Imu chose murder because Queen Lily refused to join them in the Holy Land and become a mindless Celestial Dragon for their benefit, but they couldn't let her go either becuase by that point Queen Lily already knew the ugly truth. Queen Liliy might have exposed the truth in her letter that was passed down, which is why generations of the Nefeltari Family refused to join the World Government. King Cobra came to the Gorosei during the Reverie to confirm Queen Liliy's whereabouts and the secrets of the World Government that she exposed in her letter, he did it now because he believed he was on death's door anyway and didn't fear the repercussions. Imu and the Gorosei have no choice but to murder King Cobra to keep the secret. Then they conveniently blamed his murder on Sabo during the Revolutionary Army's operation to free Kuma during the Reverie and was about to silence and kill Vivi too.