It may be helpful to divide this sentence into shorter parts. Alternate translation: "But Yahweh was very kind to the Israelite people. He helped them"
Yahweh's covenant is the reason he did not destroy Israel. This can be made explicit. Alternate translation: "This is the reason that Yahweh did not destroy them" or "Because of his covenant, Yahweh did not destroy them" (See: [[rc://en/ta/man/translate/figs-explicit]])
Yahweh's rejection is spoken of as if he had physically driven Israel away from where he was. Alternate translation: "has not rejected them" (See: [[rc://en/ta/man/translate/figs-metaphor]])