Concur is simply software which enforces a given employer's travel rules. It sits as an overlay for your employer's travel department / corporate TA.

DL is strictly enforcing the $50 fee because the entire point of its corporate program and discounts is to have the work done by the corporate customer. When you call DL to make changes, it is actually more work than a simple booking. Thus, the $50 fee.

The problem is easily solved as the employer can quite easily establish one of two systems which work seamlessly and well. Either two cc's are used. One the corporate card (or other account) and the other a personal cc which the employee who wishes to, may supply. In this case, the $300 premium for the J fare would be charged to the personal cc. Alternatively, the $300 can be charged off as a debit to the employee's compensation (again, with the employee's authorization).

The first option (personal CC) can easily be handled and is virtually cost-free. The second, does create a bit of back office accounting, but not much with any sophisticated system. Both have the advantage of keeping employees happy at close to no cost to the employer.