'Naturalism or theism' is a false dilemma - there are many other options on the table (e.g. you find non-naturalists about maths, modals, and morals who are not theists, for example; there are also all sorts of theisms to consider other than the *particularly* implausible omnipotent omnibenevolent Judeo-Christian God).
Most folks who reject religious monotheism reject it, not because they're wedded to scientism, naturalism, or some other philosophical or metaphysical -ism, but for much the same reasons they're skeptical about fairies, ghosts, and a flat earth - they think there's little evidence for, a great deal of evidence against (e.g. the evidential problem of evil, the problem of divine hiddenness). They also think there are good grounds for being skeptical about religious (fairy/ghostly) experiences.
If this is where your atheist is coming from, refuting naturalism, scientism, etc. is unlikely to make them look much more favourably on religious theism, no more than it's likely to make them look much more favourably on the existence of fairies and ghosts. From their perspective, in each case, arguments about the truth of naturalism and scientism are a largely irrelevant side-show.
Actually, it's probably not atheists who are the main intended audience for theistic arguments targeting naturalism and scientism. The intended target is *other theists*, who will likely reassure themselves that their worldview can't be *so* unreasonable because, after all, naturalism (scientism, etc.) has been refuted, or shown to be deeply suspect.
In other words, framing the God debate in such terms is often a smokescreen device.
PS. I should add that those atheists who insist on framing the debate over the existence of a worship- and gratitude-worthy God in terms of theism vs naturalism are creating an unnecessary hostage to fortune.
The image is Evil God, our omnipotent, omni-malevolent creator. There's no point kissing his behind or praising him to the heavens - he's going to torture you anyway.