If I remember correctly, MLB didn't start suspending players for steroid/HGH use until 2005 (I'm sure someone will fact-check me on that) - before that, they didn't want you to do it but if there's no penalty for doing something there's no way you can say it's wrong. So, anyone juicing before 2005 was playing within the rules.
I think of it like aluminum bats. Say that aluminum bats were used, but discouraged, until 2005; then, in 2005, they were officially banned and you got suspended for using them. Would all players who used aluminum bats before 2005 be ineligible for the Hall?