Gen 1:2 consists of three sentences in the Hebrew. Here is my literal translation:
A: And the earth/land was formless and empty
B: and darkness [was] over the face of the deep תְּהוֹם (tehom)
C: and the Spirit of God was hovering over the face of the waters
The word תְּהוֹם (tehom) almost always refers to the depths of waters or ocean - see appendix below; thus it also does here as can be seen from the unmistakable parallelism above in B & C.
Now, the fact that "over the deep" is parallel to "hovering over the face of the waters" does not necessarily imply that "darkness" is parallel to "Spirit of God" (although that is not precluded). The literary function here is more profound - the important idea in Gen 1:2 is about the "tohu and bohu" = "formless and empty".
That is, we have a picture of a formless and empty world with a churning sea/ocean described by the "deep" from the root meaning surging chaos. BUT, by complete contrast, the Spirit of God is described using a verb used of a mother bird hovering above the nest as she feed her young.
Thus, the literary intent of Gen 1:2 is to contrast the chaos of the earth with the approaching presence of God, whose first act (V3) is dispel darkness. Thus, "Spirit of God" cannot imply darkness.
APPENDIX - BDB entry for תְּהוֹם (tehom)
1. deep, of subterranean waters, Genesis 49:25 (poem in J; opposed to שָׁמַיִם), Deuteronomy 33:13 (opposed to id.); ׳רַבָּה מַעְיְנוֺת ת
Genesis 7:11; Genesis 8:2 (P; "" אֲרֻבֹּת הַשָּׁמַיִם), ׳עִינוֺת ת
Proverbs 8:28 ("" שְׁחָקִים), Job 28:14; Job 38:16 (both "" יָם);
תְּהוֺם רַבָּה Amos 7:4 (probably), רַבָּה ׳מִשְׁמָּטֶיךָ ת Psalm 36:7
(opposed to אֵל צִדְקָֽתְךָ כְּהַרְרֵי), Isaiah 51:10 (perhaps); so
plural תְּהֹמוֺת, Proverbs 8:24 ("" מַעְיָנוֺת), Proverbs 3:20
(opposed to שְׁחָקִים), and probably Psalm 33:7 ("" מֵי הַיָּם), Psalm
135:6 ( + יַמִּים).
2. (deep) sea, overwhelming Tyre Ezekiel 26:19 ("" הַמַּיִם הָרַבִּים), roaring at theoph. Habakkuk 3:10; in General, "" יָם, Job
38:30 (׳מְּנֵי ת); "" מַיִם Jonah 2:6; alonE Job 41:24; figurative,
קוֺרַא ׳אֶלתֿ ׳ת Job 42:8 ("" מִשְׁבָּרִים, גַּלִּים; but possibly
here of Jordan, compare (4); in plural = abysses of sea, Exodus 15:5,8
(of Red Sea, so) Isaiah 63:13 "" Psalm 106:9; Psalm 77:17; also Psalm
78:15 (in simile), Psalm 107:26 (poetic of hollows of great waves,
opposed to שָׁמַיִם); vaguely, כָּלתְּֿהֹמוֺת Psalm 135:6; Psalm
3. primaeval ocean, deep, in Hebrew cosmogony, ׳מְּנֵי ת Genesis 1:2 (P; "" מְּנֵי הַמַּיִם), Proverbs 8:27 ("" שָׁמַיִם), Psalm 104:6.
— (compare, further, GunkSchöpfung u. Chaos 21 ff. O C Whitehouse
Hast. DB COSMOGONY ZimKAT3. 492 f., 509 f., 585).
4. deep, depth, of river Ezekiel 31:4 (Nile; "" מַיִם, + נַהֲרוֺתֶיהָ), Ezekiel 31:15 ("" id.); plural of bursts of water
fertilizing Canaan, יוצאים בבקעה ובהר Deuteronomy 8:7 ( + עֲיָנֹת,
נַחֲלֵי מַיִם). — On Psalm 42:8 see 2.
5. abyss (si vera lectio): תְּהוֺמוֺת הָאָרֶץ = Shejôl, Psalm 71:20, but Ol We תַּחְתִיּוֺת.