Historic integrity is a tricky issue. You need to first determine if the property is indeed of historic significance. If you are asking your question in the legal sense of historic signficance, you should consult your State Historic Preservation Officer (SHPO). Contacts here:
From a practical matter, substituting plywood or new boards planed to match the thickness of the subfloor in you home should not be a problem. You need to decide the expense you are willing to tolerate to maintain integrity of a surface that is not visible except by looking up through the joists from the basement. But if you want 3 inch x 5/8 oak boards, those are certainly available or can be easily fabricated from 3/4 inch stock using a planer. Based on what I have seen in historic preservation determinations, the visible attributes of a home, such as trim and finish treatments are much more important than structural repairs such as the subfloor. But if the property is historically signficant, contact the SHPO. They are usually very conservative in their advice and willing to provide information like this.
Just curious, what did you use for the joist repair? I assume modern planned softwood lumber.