I guess language would also depend on the history of the world you're working in. If there was some sort of cultural rebellion against religion in the past, it could be plausible that a large portion of religious references could have been violently stricken from the culture. If the aggro was aimed at a specific religion, then it would be likely that other religious systems wouldn't have been as affected so leaving the days of the week would be okay, but imploring upon Christ could result in some seriously bad juju.
If it's that far in the future who knows what religious structures would exist? I just have trouble imagining a society of humans that has no concept of something larger than itself. Even in agnostic circles that's true, though they've elevated popular science into the role.
Well, using/inventing phrases, that originated from/due religion is fine for me. Phrases where the religious origins are vague, or even not noticeable at all, are by no means off the table. I just want some phrases, that have no religious origins at all, which is the part that kinda gets more difficult then I had anticipated. I haven't worked out many details on that, but rebellions might happened against tyrannical/fanatic religions, but there will be no major rebellion against religion in general in the past. In my setting, religion just faded out of society, mostly that is. Religion isn't completely gone, there are still a handful religions present, though, none of them is big enough to be known throughout the entire galaxy. Besides, there was already enough turmoil around religion in the past, so there is a likely hood that most of us have learned the lesson of it. This could mean, that such turmoils around religion might be far and few in the future, regardless if religions will fade or not.
With an atheist society, maybe they would use figures in science history? Like in some of my writings I've used "by the Saturn rocket, you're gullible!" And "I swear to Glen!" (John Glen)
How about giving it some rhyme and letting the reader connect the dots? Oh, Lord! = Oh, Lard! Bloody Hell! = Bloody Spell! Jesus Christ! = Rezus Heist! and of course: Oh, my God! = Oh, my Goat!
Exclamation! Science, bitch! Woah, boomer! Call of Cthulhu Oh my Spock Oh my Harry Potter Oh my Chewbacca Holy Dark Lord By Toutatis! By Belenos! By Zeus! By Jupiter!
We say meaningless things in Turkish like "Amaan!" or "Yaaa!" that are non-deity-related, in fact using religion to swear by is not done at all unless it's a foreign translation e.g. in a movie. It would depend really on the type of society you are writing about. You'll also have to decide whether they have any remnants of belief from earlier times. Language can take a long time to evolve.
By the sting of the stars! What in the theologian! Darwin! Oh my void! Son of a chrysalid! By the matter! Oh my energy! By gravity! My orbit you are round-headed! Frauck! By the man's reproductive organ! Oh how splendidly servile our situation is! By the disregard of the universe, how cold you are! Through unremitting discourse, your remarks refurbish my refrain! There shall be no place for such swindling subversion of the subject at hand! By the gallants of the sun warriors, your solar exodus has left me in contemptible shade!
Not necessarily though. I would suggest that as society becomes more religious number of such phrases increases (more inspiration), but usage by individuals decreases. In Croatia, which is allegedly Catholic, we have fun phrases ranging from "God save" to "may the God f*** you". But individuals who actually are religious, or even just raised in religious families, will rarely use something harsher than "go into figs"/"go to figs".