While P.E.D.'s were against the rules even before testing, the rules had no language that allowed for scores and statistics to be vacated. We have no means of officially discounting them, which means Bonds is the record-holder, and 1998 exists in the books.
And while I think Ruth is the greatest, it's fair to point out that he played pre-integration, and we know from the success of some of the black players that joined the majors once they were allowed that the talent level of the competition did improve overall.
I don't think there's a way to determine which records to asterisk.