The thing is, it is not the soul or atma which is bound by maya, but it is the jivatma which falls prey to it. Atma means the true self devoid of mind, body and senses and jivatma means atma along with mind, body, senses, etc. which can be gross or subtle.
The living entities in this conditioned world are My eternal fragmental parts. Due to conditioned life, they are struggling very hard with the six senses, which include the mind. [BG - 15.7]
Atma can be considered as a spark of God which is eternal and ever free, but apart from this jiva shakti, God has another energy potency known as prakruti or maya. Jiva shakti and maya shakti being energies of God are also eternal. And from this prakruti or maya alone originate the mind, senses, etc. When these two energies associate jivatma is formed and because mind is made from prakruti it has natural attraction and inclination towards prakruti. Hence, it is the mind alone who is naturally a prey of maya, not the atma. That is why it is said, mind alone is the cause of bondage and liberation:
mana eva manuṣyāṇāṃ kāraṇaṃ bandhamokṣayoḥ [Brahmabindu Up. - 2]
- Mind alone is the cause of bondage and liberation of man.
So in brief, the soul is ever free as it is irrespective of whether it lies in the body or somewhere else. It is the mind which is in bondage. So when Gita speaks of the indestructibility of the soul it is referring to atma and else where when it is said the soul is in bondage it means jivatma, the embodied being. Please contemplate over the verses of chapter 13 and the following verses of Gita as well: 7.4-5, 15.8-9. Also please refer to this answer for some more info about maya and how it affects the jiva.
And regarding God taking incarnations, there are multiple reasons behind it apart from teaching lessons to the jivas which you can read in this answer.