Does it occur to you that the institutions you agree with will also suffer?
Aren't you also a bit hasty? These are centuries old institutions, which have become problematic (from your standpoint) only recently. It is not the insitutions, therefore, but some aspects of our culture that are problematic. Your suggestion amounts to throwing away an apple because it is unwashed.
Harvard has an endowment in the tens of billions of dolalrs, but it still has been raising tuition faster than inflation for decades. Why does should this rich instititution pay zero capital gains and income taxes from its investments? If it paid taxes on investments, maybe it would less active in advocating higher investment and income taxes for others.
To avoid hitting small institutions, you could say that the first $1 billion of an endowment can be invested tax-free.