So this question is far too broad for me (or anyone else probably) to answer fully. It depends what you mean by being "acceptable", where in Europe you are, what facet of life are you talking about etc. For instance, there are places in Europe NOW where being atheist is not socially acceptable.

That caveat said, I'll give a partial answer but it will be limited to English academic censorship and legal suppression (my primary study is history of philosophy). My answer will draw from David Berman's A History of Atheism in Britain as well as primary philosophical sources like Hobbes, Hume, Russell etc.

One thing to note, Atheism was usually not specifically outlawed by name. What was more common was the outlawing of blasphemy or heresy. Berman hypothesizes that this is due to an effort to avoid openly fighting atheism- instead focusing on more traditional foes while all the while outlawing atheism implicitly with the formulation of the law. Famous laws outlawing blasphemy were on the books well into the 20th century (For instance the Blasphemy act of 1697 was not abolished until 1966) and these laws were enforced well into the 19th century.

To start answering your main question- the last executions for heresy and blasphemy both occurred in the 17th century. This time period also saw the first true forays of British intellectuals into atheism. In the academic sphere, one of the first people to be regarded as a tolerated atheist was Thomas Hobbes (who is sometimes regarded as a closet atheist though there’s reasonable doubt given that 2/3 of his primary work Leviathan is concerned with Cristian scripture and religion and his protestation against the label). In the 18th century we see academics being denied university positions and having work suppressed for fear of rocking the religious boat. For a famous example take Hume who not only was denied academic appointment throughout his life (even though he had published extremely successful works in both philosophy and history) but also was too afraid to publish his main work on religion The Dialogues Concerning Natural Religion until after he died. He set up three people to publish his work if the previous should fail and the work was only published by the third person! So we can safely assume that anti-atheist prejudice was well alive in the 18th century (even in the late century when the dialogues were published).

Atheism gained a rapid foothold in the British academic life in the 18th century, though censorship and prosecution was still common. Finally, by the turn of the 20th century we see unabashed militant atheists such as Russell, Moore and McTaggart who openly (and relatively without censure) profess atheism.

So to put a long story short, I see the acceptance of Atheism in academic circles as a gradual process from the first covert atheists of the 17th century to the outspoken militant atheists of the turn of the 20th Century.