What would be a word or phrase to describe a religion without a deity?

How about ideology?

M-W:

ideology: 2 a : a systematic body of concepts especially about human life or culture b : a manner or the content of thinking characteristic of an individual, group, or culture c : the integrated assertions, theories and aims that constitute a sociopolitical program

I understand that your mostly-women time travelers are followers of "Mother Universe", but at a higher level, independent of the content of their beliefs, they are trying to inculcate in humanity a specific ideology, in their case an ideology whose aims are "to curtail or prevent (through education and social traditions) overpopulation and pollution in future Earth".

Aside: An absolute belief in the ability of science to solve all of our problems is a religion in disguise, just another form of metaphysics.

"A religion without any supernatural elements" seems contradictory. Religion by its typical definition is faith-based and contains supernatural elements, even without belief in a deity. While it still has a non-scientific supernatural element (belief in souls), a close real-world religion that is nontheistic is Jainism. If you're willing to set aside the "absolutely science-based" part of your description and focus on the details in the edit, Jainism could be used as (or at least compared with) the women's religion.

I contend that a fully science-based [word OP is looking for] is more of a philosophy rather than a religion, but philosophy may be too vague.

To be more specific, we could call the set of concepts they are trying to introduce a

worldview¹

1 the overall perspective from which one sees and interprets the world

2 a collection of beliefs about life and the universe held by an individual or a group

Even more suitable than worldview, we have an excellent loanword from German:

Weltanschauung²

• a comprehensive view or personal philosophy of human life and the universe (Collins English Dictionary)

• a comprehensive conception or image of the universe and of humanity's relation to it (Webster's College Dictionary)

The women in the story want to create a worldview/Weltanschauung whose tenets will curtail or prevent overpopulation and pollution in future Earth.