INA comprised of deserters of British Indian Army so it was not considered appropriate to incorporate rebels back in the professional army. Though Nehru did this under pressure from Allies but in hindsight this decision seems to be beneficial as Indian Army was the only Army in Indian Subcontinent which remained apolitical and professional in next 6 decades.

I am not aware of any official justification. I feel the reason might be that members of such liberation armies are motivated by rebellion. Regular professional armies are not comfortable with such people. They might find it difficult to comply with the kind of disciplined behaviour which the army demands. For the same reason Bangla Desh did not incorporate Mukti Bahini into its regular army and Pakistan would not admit people from its various militant organisations into its army.