Brihad Aranyaka Upanishad's Adhyaya 6; Brahmana 4 is describing rites and rituals for obtaining good progeny for couples. The rites are to be followed by the husband and wife who are seeking particular types of off-spring.
For example, 6.4.15 is saying that if the couple wishes to have a male child having yellowish complexion, who will be well read in two Vedas and would live long must cook curd mixed rice and consume it with Ghee.
6.4.16 is prescribing the consumption of a preparation of rice cooked with water with Ghee for obtianing a son having particular features and qualities.
For obtaining a scholarly girl child, 6.4.17 is prescribing a preparation of rice mixed with sesame seeds to be consumed with Ghee.
And, 6.4.18 is similarly giving the required diet for a couple who wishes to have a son having particular qualities.
The first verse of this Brahmana is to read to understand what this particular chapter is going to teach.
eshAm vai bhutAnAm prithivi rasah prthivyA ApohapAmoshadhaya
oshadhinAm pushpAni pushpanAm phalAni phalAnAm purushah purushasya
The essence of all beings is the Earth; Essence of Earth is water;
Essence of water are plants; Essence of plants (Oshadi) are flowers
(pushpa); Essence of flowers are fruits (phala); Essence of fruits is
Purusha or man; And, the essence of Purusha is retah (or Shukra or
Since, essence of man is Shukra and the type of offspring to be born depends on (the quality of) Shukra, hence this Brahmana is prescribing, as part of the ritual, different types of diets to be consumed to obtain certain types of off-spring.
So, here meat eating is not just for pleasure but for a sacred purpose and is part of a ritual. And, it is sanctioned by the scriptures.
Manu Smriti 5.43. A twice-born man of virtuous disposition, whether he
dwells in (his own) house, with a teacher, or in the forest, must
never, even in times of distress, cause an injury (to any creature)
which is not sanctioned by the Veda.
5.44. Know that the injury to moving creatures and to those destitute of motion, which the Veda has prescribed for certain occasions, is no
injury at all; for the sacred law shone forth from the Veda.
On the other hand, the Atharva Veda mantra must be talking about meat eating that is not sanctioned by scriptures, which are done without sacred motives but just for the sake of pleasure.
When meat eating is part of a ritual and is for a sacred purpose it is allowed in Hinduism but outside of rituals meat eating is never recommended. So, there is no contradiction here according to me.