Personal deprivation aside, to let employees (government or private enterprise) keep the miles from flying on their employer's expense is not a right. It's a perk.
For a company, it means the travel department can't use the miles to reduce their overall cost of operations. It means the same for government departments. Every personal trip or upgrade you, as an employee, receive is money out of the employer's pockets.
So as a government employee, you don't own those miles directly except as part of the taxpayers of America. It's up to us, collectively as a countyr, to decide whether to grant an additional perk to government employees.