How do exegetes who do not believe in metaphorical interpretation of the Qur'an explain verses such as: (They put their fingers in their ears from the thunderclaps for fear of death) and (Then We breathed into her of Our spirit) without interpreting them metaphorically?

The majority of scholars consider that metaphor (majāz) exists in the Arabic language, the Qur'an, and the Sunnah. When there is a disagreement on an issue, the matter is relative, and one must adhere to the Qur'an and the Sunnah.

Regarding the verse, "They put their fingers in their ears," those who deny metaphor believe that the context indicates the intended meaning, and that what is meant are the tips of the fingers (the fingertips) to exaggerate their flight, and it does not mean inserting the entire finger. Sheikh Ibn 'Uthaymeen holds that there is no metaphor in the verse, as "fingers" is a plural referring to their action of "putting," and the addressed person would not understand it to mean inserting the entire finger.

As for His saying, "Then We breathed into her of Our Spirit," the intended spirit is Jibreel, who breathed into Maryam by Allah's command, and it is not from Allah's own essence.