No, this is not a particularly well argued or serious article. If anything, it seems to be a somewhat trite and muddled repackaging of Gimbutas' (universally discredited) theory that the pre-Indo-European populations of Europe worshiped a universal "earth goddess" deity an were peaceful and matriarchal.

There are also quite a few simple factual errors or absurd interpretations. For example:

Which all helps to explain a conundrum that has long bothered me. At the birth of society and civilisation I find a religious landscape littered with feisty female deities who make wisdom their business. There's Nisaba the Babylonian goddess who looks after the stores of both grain and knowledge in Mesopotamia; the Hindu goddess Saraswati; the Zoroastrian Anahita; the ancient Greek Athena; and the Shinto Omoikane (a fine goddess of holistic thought and multitasking).

But come the end of the bronze age and many of these deities have been demoted. Here we witness a precursor of the Judaeo-Christian scenario. Up until 1400BC, citadel settlements are stable. Goddesses – notably in charge of fertility and learning – have a crucial role to play. But as civilisation gets greedy and society more militaristic, these wise women are edged to the sidelines in favour of a thundering, male warrior god. Just the kind of chap to lead raids on neighbouring citadels – a historical fact we witness in the brutalised archaeology and stockpiles of traumatised human remains: thousands of men whose bones are now emerging from digs across the eastern Mediterranean, north Africa and the Middle East – cross-hatched with axe-cuts, their skulls pierced with arrows, their chests with spears.

Athena only really rose to prominence after the Bronze Age (and particularly connected with the rise on Athens' military power), Omoikane, Anahita and Saraswati are very firmly post-Bronze Age. Nisiba does actually substantially exist prior to 1400 BCE, so there's one--although she is Sumerian, not Babylonian. I don't know of any evidence to suggest that before 1400 BCE there was peace and afterwards there was war.

And this mystical "σοφια" she goes on about is just the Greek word for wisdom or skill, not some mystical statement of feminine whatever.

Honestly, this article belongs in /r/badhistory.

fitting facts into a narrative

You've just described what historians do. All historians have a 'project' -- something they want to say. Evidence is selectively emphasized or downplayed to help make the historian's larger point. How well evidence is presented and later, accepted, determines how successful a historian is in completing their project. Some historians are much better than others in making their work appear less personal-narrative-driven, but it's always there.

With respect to the piece you linked, it doesn't appear to purport to be anything other than commentary. That's of course fine, but it's not often considered scholarly. Also, given the article's length, it cannot possibly develop this (or nearly any) topic well enough to be a good analysis.

That's not to say it's without merit. Far from it. It's provocative and at least superficially informative. That's better than the vast majority of stuff on 'news' sites.