Perhaps more than science, free will justifies atheism...

• No religion has scientific evidence behind it, which is a large motivating factor for some atheists to become or remain atheists. However, perhaps instead of science “justifying” atheism, it is just a supporting element or it, and the larger encompassing element is free will.
• Whether for better or for worse, free will does allow us to choose whichever belief system suits us best. If one chooses to be Lutheran, for example, it (hopefully) is because of their own free will. Same with Buddhists, Evangelicals, Hindus, agnostics, atheists, and beyond. Of course, family pressure and tradition can cause some to feel forced into a religion, but the point here is that nothing can truly justify a belief system except the fact that someone wants to follow it.
• This argument can, of course, head down a slippery slope because free will can also be used for extremely bad things (ie: murder, rape, theft, etc.) However, when talking about religion or lack thereof, free will may be a good viewpoint for justifying whichever religion you do or do not adhere to.

Science can justify atheism. But it's not on atheism's 'side' in that it doesn't necessarily disprove theism.

• Science kind of justifies evidential atheism. Anthony Flew talked about this as being how the default position for any believer should be neutrality about God's existence. And this amounts to atheism: "[The onus of proof lies on the man who affirms, not the man who denies."] (https://iep.utm.edu/atheism/) It's atheism by default: which is naturally reversible if proof for God's existence arises.

• However - science also doesn't necessarily disprove a religious belief. It's a way of knowing that's different from other ways in that it's entirely dependent on empirical/material evidence. The atheist who takes this evidence as the only acceptable proof for something's existence can thus justify their lack of belief. But [supernatural beings like God can't be held to such an evidential standard] (https://www.national"academies.org/evolution/science-and-religion), so many religious groups accept scientific findings alongside their understandings of God.