Milah rectifies the Tree of Knowledge

במדרש סוד ה' ליריאיו ובריתו להודיעם דורש על המילה.

In the Midrash, the pasuk "The secret of Hashem is for those who fear Him, and His covenant to make them know" (Tehillim 25:14) is expounded as referring to the mitzvah of milah (circumcision).

The Sefas Emes opens by noting that Chazal connect this pasuk's "secret" and "covenant" specifically to bris milah.

כי סוד ה' הוא התורה שנקראת עץ חיים.

For "the secret of Hashem" is the Torah, which is called the Eitz HaChaim (Tree of Life).

The first phrase, "the secret of Hashem," points to Torah — the wellspring of life, the Tree of Life itself.

וברית הוא כלל התרי"ג מצות שהם תיקון עץ הדעת לכן יש מצות עשה ומל"ת.

And "His covenant" is the totality of the 613 mitzvos, which are the tikkun (rectification) of the Eitz HaDaas (Tree of Knowledge) — and that is why there are both positive mitzvos and negative mitzvos (lo saaseh).

If Torah is the Tree of Life, the mitzvos are the repair of the Tree of Knowledge of good and evil. Since that tree blends good and bad, its tikkun naturally splits into "do" (drawing toward good) and "do not" (turning from bad).

ולכן במילה יש ערלה כי שם שורש עץ הדעת דאין קשוי אלא לדעת.

This is why in milah there is the orlah (foreskin), for there lies the root of the Eitz HaDaas — as Chazal say, "there is no arousal except through 'daas' (knowing)."

The bris is performed at the very place connected to the Tree of Knowledge; the orlah represents the unrefined element of that tree, which must be removed to accomplish its tikkun.

כי הנשמת חיים באדם חלק מעץ החיים.

For the nishmas chaim (breath of life) within man is a portion of the Tree of Life.

Man's living soul is itself a piece of the Eitz HaChaim — the inner point of life that flows from Hashem.

אבל בברית הוא המשכת החיים לטוב ולמוטב.

But in the bris, it is the channeling of that life for better or for worse.

The covenant of milah governs the place where the soul's life-force is drawn down into the world — and there it can be directed toward good or, chas v'shalom, the opposite. That is why it requires a bris of tikkun.

ולכן מילה קודם לכל המצות:

Therefore milah precedes all the mitzvos.

Because it rectifies the very root of the Eitz HaDaas, the place where life is drawn into the world, bris milah comes first and underlies all the other mitzvos.

Summary: "The secret of Hashem" is Torah, the Tree of Life, while "His covenant" is the 613 mitzvos that rectify the Tree of Knowledge. Bris milah works at the very root of that tree — the place where the soul's life-force is channeled into the world for good or ill — and by removing the orlah it accomplishes that tikkun. For this reason milah takes precedence over all other mitzvos.