Doctor vs Time Lord Hypocrisy.

“The policy of the Time Lords is clear. strict non-intervention in other worlds and times. However, policy and reality sometimes diverge. There are times when it is necessary to intervene. That is the purpose of The Division.” - The Timeless Children.

“Not every civilisation works or is enlightened. Some require help. Some needed to be told. Division assessed and acted accordingly.” - Tecteun, Survivors of the Flux

The way Thirteen gets so angry learning that Division, this shadow organization that started in Gallifrey interfered. And the Doctor was punished for interfering, for helping people.

The Doctor wasn’t punished because she interfered as @jod13whittaker pointed out, the Doctor was punished because she didn’t interfere in the right way.

The right way being– interfering for the Glory of Gallifrey. The Glory of Time Lords.

And this isn’t the first time this was broached in the extended universe, Rassilon apparently did genetic edits in the universe so other aliens would look more Time Lord.