Turn 'em and Burn 'em
This will work exactly as described in your question. True Polymorph is concentration, so that will use up your concentration during this event. Turn Undead does NOT require concentration, so you can just as easily Destroy the Undead (which, given your ability to cast True Polymorph), shouldn't be a problem in terms of CR.
True Polymorph includes the clause:
If it reverts as a result of dropping to 0 hit points, any excess damage carries over to its normal form.
You have invested in your 9th level spell and gotten lucky in the failing of saving throw for it by the Kraken. Normally, getting to 0 HP would return the Kraken to form, but Destroy Undead doesn't kill or bring a creature to 0HP, it destroys them and bypasses the 0HP issue.
This encounter began with a Kraken, and ended with the defeat of the Kraken. Even though you True Polymorphed the Kraken into a lower CR creature, you still defeated the Kraken. The True Polymorph Skeleton->Destroy Undead was HOW you killed the Kraken. Because of this, you should get credit for your ingenuity and luck and get the XP for a Kraken.
But I could see a DM saying that you killed the Skeleton, not the Kraken. When you True Polymorphed the Kraken, it was no longer a Kraken and never became a Kraken again. And it died when it was a skeleton and still never reverted.
The DMG does state:
Each monster has an XP value based on its challenge rating.
While the end state was a different CR, I would not agree with this and base the XP off the original encounter and not what a player did to defeat the creature. Punishing a the player for the use of their highest spell slot, clever tactics, and a lot of luck doesn't seem right.