See Gen 25:23. Representing their respective nations, as often in the Old Testament. Num 23:7, Num 23:10, Num 23:23; Num 24:5; Jer 49:10; compare also the original of the citation, Mal 1:2, Mal 1:3, the burden of the word of the Lord to Israel. Compare also Edom in Mal 1:4, synonymous with Esau in Mal 1:3; and Israel, Mal 1:5, synonymous with Jacob, Mal 1:2.
Hated (ἐμίσησα)
The expression is intentionally strong as an expression of moral antipathy. Compare Mat 6:24; Luk 14:26. No idea of malice is implied of course.