There is a fundamental difference between HE and IL.
1. HE -- In English, to determine whether to use HE/SHE/IT, you go to the real world first, and look at the physical sex for whatever the noun refers to. Although God is not a biological being, Christians view God as the "father" and Jesus as his "son", meaning they think of God as male (for right, wrong, or indifferent).
2. IL -- In French to determine whether to use IL/ELLE, you go first to the noun (the actual word, the string of letters or string of sounds) that labels whatever is referred to, not to the real world. GOD - is labeled by DIEU in French, which is a masculine word. It can refer to male or female gods, or to a god without physical sex whatsoever. (note: déesse, also exists, which refers exclusively to a male god). Dieu, though, does not have to refer to a male deity.
3. Therefore, it is perfectly natural to refer to DIEU as IL (as a simple subject) in French. It does not automatically imply male sex, unlike the word HE.
4. note: for people, the grammatical gender of a word often matches the physical sex of the person, but not always. It doesn't have to do so. If you refer to a man as a personne (person), because personne is feminine, you use feminine words to describe that man, until you use a different noun with a different grammatical gender (such as homme for man, or the person's name, where the grammatical gender matches the physical sex).
5. note also: Because every noun in French is grammatically feminine or masculine (there is no neuter), the default grammatical gender (for example, in situations where you normally match the physical sex, but there is no physical sex, like using Yahweh/Yahvé as God's name), is the masculine gender (because it's shorter than the feminine one).
6. in other words: HE and IL -- are not exactly the same. HE - physical sex; IL - grammatical gender; they are fundamentally different (although related) concepts.