I believe you answered your own question without realizing it.
Referring to:
Isaiah 54:6 "For the LORD has called you like a wife deserted and grieved in spirit, like a wife of youth when she is cast off, says your God"
This verse plainly speaks to the metaphor, ie "the wife of your youth" is likened to God Himself. Malachi 2:14 is an example of this metaphor. Most people get stuck in Malachi chapter 2 thinking that God is speaking primarily about Israel's divorcing practices but this was not the main issue in that chapter. If you go back and read the entire context, you'll see that God was dealing with Israel on their idolatry.
Malachi 2: 11-14
11 Judah hath dealt treacherously, and an abomination is committed in Israel and in Jerusalem; for Judah hath profaned the holiness of the Lord which he loved, and hath married the daughter of a strange god.
Note the use of the singular here "married the daughter (sing) of a strange god (sing). The use of the singular tells us that God is dealing with the nation of Israel about their idolatry in general. There is not one specific strange god implied here.
12 The Lord will cut off the man that doeth this, the master and the scholar, out of the tabernacles of Jacob, and him that offereth an offering unto the Lord of hosts.
Israel was guilty of going after other gods and then coming back and attempting to be blessed by God by offering sacrifices.
13 And this have ye done again, covering the altar of the Lord with tears, with weeping, and with crying out, insomuch that he regardeth not the offering any more, or receiveth it with good will at your hand.
Then when no blessings would come to Israel, verse 13 says Israel would cry over the altar, wondering why they wouldn't get the blessing from God.
14 Yet ye say, Wherefore? Because the Lord hath been witness between thee and the wife of thy youth, against whom thou hast dealt treacherously: yet is she thy companion, and the wife of thy covenant.
In verse 14 God tells them why. Israel is guilty of cheating on the Lord, cheating like a husband cheats on a wife. Please note the phrase, "and the wife of thy covenant". This is a clear reference to the covenant relationship between God and Israel.