Alibaba has a unique governance structure, very different than that of the typical public companies. It's kind of like a partnership. Owning a big chunk of the Alibaa shares does not automatically give one the equal say in running the company.
This is what I can find about it in English:
Basically, Alibaba is run by a steering committee whose memeber are the managers of Alibaba and its related companies. What makes this steering committee special is that its members can "nominate majority of the board of directors".
Alibaba was not punished because of the foreign ownership. It was their monopoly practices that ran at odds with the Chinese government's new priority: social equality.
The foreign owernship in Alibaba are the unfortunate result of shortsight of Chinese domestic investors in the early days. It is said that they all turned their back on Jack Ma. He then had to look for the needed funding abroad. I think Tencent has the same story, too.
The investors, regardless of their allegiance. deserve the return from their investment. This is simply how the game plays.