Sending Away The Mother Bird

There is a commandment to send away a mother bird before taking away their children (Deut. 22:6-7):

If a bird's nest happens to be before you along the way, in any tree or on the ground, with young ones or eggs, with the mother sitting on the young or on the eggs, you shall not take the mother with the young; you shall surely let the mother go, and take the young for yourself, that it may be well with you and that you may prolong your days.

The Rambam (Moreh Nevukhim 3:48) famously explains that the reason for this commandment is compassion for animals. This is problematic because it contradicts an explicit Mishnah (Berakhos 5:3) which says that we silence a prayer leader who says "Your mercy reaches a bird's nest [and should reach us as well]", implying that God's mercy on a bird is not the reason for this commandment. In the Gemara (Berakhos 33b) there are two views of why this declaration is problematic: 1) it implies that birds receive preferential treatment over other animals (which the Meiri explains means that it implies that there is individual providence for animals), or 2) it suggests that the reason for this commandment is God's mercy rather than just being a divine decree. (Cf. R. Natan Slifkin, Man and Beast, pp. 127-129.)

The Rambam addresses this by saying that he follows the former view, and not the latter that this commandment is not about God's mercy.

R. Joseph B. Soloveitchik is quoted as offering the following explanation of the Rambam (R. Abraham Besdin, Man of Faith in the Modern World, p. 97):

Maimonides' view is contradicted by the Mishnah... This is understood as referring to a public reader, sheli'ah tzibbur, who in leading a formal prayer service says: "Just as You have compassion on the mother bird in the mitzvah of Shilu'ah Hakan, so be You compassionate with us." Such manner of formal prayer is not permitted because it is based on an assumption that compassion is the reason for the mitzvah. This cannot be accepted with certainty, and it is wrong to render a prayer in behalf of the community contingent on an uncertain hypothesis.*

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* In private prayer or in sermonic interpretations of a text, such would not be prohibited.

In other words, the problem in the Mishnah is that the reason for the commandment is included in a public prayer, which assumes the reason to be certain. I saw a similar explanation offered in the name of Rav Kook -- that it only applies to prayer -- but with a different reason that implies that it is improper even in private prayer (R. Chanan Morrison, Gold from the Land of Israel, 327-328):

When we serve God with our minds and intellect, it is proper to seek rationale for mitzvot. such pursuits contribute to the intellectual realm, to the realm of Torah study. Understanding is achieve empirically, as we try to discern the underlying principles from the myriad details. It is thus fitting to analyze each individual mitzvah, and attempt to understand its function and reason; and each individual analysis will then contribute to our overall understanding of the Torah.

Yet, we also seek perfection in our emotional service of God. And in the emotional realm, the details tend to obstruct and confuse. Especially when we serve God in prayer, our incentive should be a general desire to fulfill God's will. This universal motivation, simple and uncomplicated, applies equally to all mitzvot.

The distinction between our intellectual and emotional service of God surfaces in the difference between Torah study and prayer. One who prayse, "May Your compassion extend to us as it does for the mother bird," is confusing what should be the straightforward, simple emotions of noble service with complex calculations regarding the underlying rationale of mitzvot...

I don't see how Rav Kook's explanation can be read into the words of Moreh Nevukhim but, I believe, R. Soloveitchik's can.