The NEC does not say that requirements should only be followed if it is convenient or inexpensive. If the original sub-panel was installed incorrectly, you MUST correct it with the new installation. IF it was installed under a code that did NOT require the grounds and neutrals to be separated, then it could be left as is. HOWEVER, I don't know that there is a code that allows a sub-panel to be installed in this manner. I have only been in the trade for 30 years or so and sub-panels have always required separate grounds and neutrals when they were in the same building. We used to be able to install a panel in a separate building with the neutrals and grounds together (used to say "new building = new service") but that is now gone. Just because something has been in violation for years and it would be hard to fix does not give you permission to leave it in violation.
I once did a service change where the original installer had used the black wires as the grounded conductor (neutral) conductors and the white wires as the ungrounded (hot) conductors. Could I put them back that way just because it had been like that for years and it was going to be expensive to correct? Of course not! It was, is, and will probably always be a violation and I had to correct it as part of my installation.