I think you have to differentiate a bit more.
The new T&Cs say this with respect to removal of content:
2. PSF May Remove Content
We have the right to refuse or remove any User-Generated Content that, in our sole discretion, violates any laws or PSF terms or policies.
The previous terms don’t include anything related to removal of content, but instead refer to the same “Acceptable Use Policy” as the new ones, and those include the clause:
Violations and Enforcement
PyPI retains full discretion to take action in response to a violation of these policies, including account suspension, account termination, or removal of content.
AFAICT, the “Acceptable Use Policy” has not materially changed, so this is effectively unchanged.
What did change is how account termination is described:
Previous terms:
Violations and Enforcement
PyPI retains full discretion to take action in response to a violation of these policies, including account suspension, account termination, or removal of content.
New terms:
3. PSF May Terminate
PSF has the right to suspend or terminate your access to all or any part of the Website at any time, with or without cause, with or without notice, effective immediately. PSF reserves the right to refuse service to anyone for any reason at any time.
In reality, I don’t think those two clauses are effectively that different (organizational policies being just a statement of intent). The new one is a standard service contract clause, which is probably why it ended up in the terms.
Please also take into account that PyPI is a service provide by the PSF to the community for free (except for the new commercial org accounts). The PSF really is free to put anything into the T&Cs it sees fit.
Of course, getting some more community feedback upfront would probably have helped, esp. since the multipage new terms are a lot more involved than the previous ones, which fit on a single page.