Wikipedia references http://www.samizdat.qc.ca/arts/lit/Pascal/Pensees_1671_ancien.pdf as being the "1671 edition with old French spelling". It contains,
Jamais on ne fait le mal ſi pleinement & ſi gayement, que
quand on le fait par un faux principe de conſcience.
So to me it looks like more than a translator liberty: more like a deliberate falsification.
But the French version which you found is simplified: it's missing "un faux principe de" ... so the atheist' English version may (instead of being a falsification) be just a misinterpretation of that or of some other simplified version.
I can't vouch for its fidelity to the original
A photo of this sentence can be found on page 271 of the First edition on Gallica.
In Wikipedia I read that the first edition was published after his death: and so I wondered whether the first edition might be unreliable. Wikipedia says,
In the 1990s, decisive philological achievements were made, and the edition by Philippe Sellier of the book contains his "thoughts" in more or less the order he left them.
So for a more modern version you might want to try to find that, which is available here (or a larger version with more background information reviewed here and available here).
I haven't seen Sellier's version, however this review of it implies that its message is approximately as you remember, i.e. not atheist in its intent:
The structure of the apology Pascal intended is best described by H. F. Stewart D.D. in the preface to his translation of the Pensees: Part I shows "from Nature" that man is wretched without God, Part II shows "from Scripture" that Jesus is the Redeemer of mankind. Part I subdivides into Ia (man without God) and Ib (man with God) to show man's inherent wretchedness. The themes of Part I are largely in the tone of vanitas mundi, after the tradition of the Hebrew Bible's book of Ecclesiastes, while the many short maxims inserted into the text are reminiscent of the Book of Proverbs.
For the non-Old-French speakers, would you care to hazard a more appropriate translation?
At the IMO slight risk of using a False friend in the following translation:
One never does evil so fully and gaily, as when one does it through a "false principle of conscience."
IMO only a atheist with no sense of history or of the text could translate or interpret "false principle of conscience" there as "religious conviction".
Other translations of "conscience" include "mind" or "awareness": it's saying that what a person thinks or believes can be mistaken.
For example the very previous paragraph to that sentence (in the first edition) gives a sense of the kind of thing he's saying,
Il y a trois moyens de croire, la raison, la coutume, &
l’inſpiration. La Religion Chreſtienne, qui ſeule a la raison, n’admet
pas pour ſes vrays enfans ceux qui croient ſans inſpiration. Ce n’eſt pas
qu’elle exclue la raison, & la coutume: au contraire, il faut ouvrir ſon
eſprit aux preuves par la raison, & s’y confirmer par la coutume; mais
elle veut qu’on s’offre par l’humiliation aux inſpirations, qui ſeules
peuvent faire le vray & salutaire effet; ne evacuetur crux Christi.. [I
Cor. 1, 17]
... which I translate as,
There are three ways to believe: reason, custom, and inspiration. The Christian religion, which alone has reason, doesn't admit as its true children those who believe without inspiration. It's not that she (i.e. the Christian religion) excludes reason and custom: on the contrary, one must open one's spirit to proofs by reason, and confirm oneself there by custom (or "habit"); but she wants that one offers oneself by humiliation (or "humility") to inspirations, which alone can make the true and salutary effect; "lest the cross of Christ be emptied" (Latin quoting 1 Corinthians 1:17).
The paragraph before that is even more telling:
Toutes les Religions & toutes les sectes du monde ont eu la
raison naturelle pour guide. Les ſeuls Chreſtiens ont eſté aſtreints à
prendre leurs règles hors d’eux-meſmes, & à s’informer de celles que
JÉSUS-CHRIST a laiſſées aux anciens pour nous eſtre tranſmises.
Il y a des gens que cette contrainte laſſe. Ils veulent avoir, comme les
autres peuples, la liberté de ſuivre leurs imaginations. C’eſt en vain que
nous leur crions, comme les Prophètes faisoient autrefois aux Juifs:
Allez au milieu de l’Église; informez vous des loix que les anciens luy
ont  laiſſées, & ſuivez ſes sentiers. Ils répondent comme les Juifs:
Nous n’y marcherons paſ; nous voulons ſuivre les penſées de noſtre
cœur, & eſtre comme les autres peuples. [I Rois 8, 20]
All the religions and sects of the world had natural reason for their guide. Only Christians have been compelled to take their rules from outside themselves, and to inform themselves with those [rules] which Jesus Christ has left to the ancients to be transmitted to us. There are some people who are tired (or "weary", "jaded", or "bored") of this constraint. They want to have, like other peoples, the liberty to follow their imaginations. It's in vain that we cry to them, as the Prophets did formerly to the Jews: go into the [middle/environment/society of the] Church; inform yourself of the laws which the ancients left (i.e. gave or transmitted to) her (i.e. the Church), and follow her pathways. They reply like the Jews: we will not walk there; we want to follow the thoughts of our hearts, and be like the other peoples.