I think the only fair way to evaluate the legacies of players that played during the steroid era is to realize that we have no reliable list of players who used PEDs with proof that they used. We do know enough to acknowledge that the use of PEDs was fairly pervasive during that era. There is hard evidence of use against very few players -- e.g. Palmiero, Bonds, ARod and Clemens, but with regard to others there is merely suspicion and innuendo e.g. Nomar. Next because there is no reliable list of who used, every player from that era should be viewed with suspicion. These decisions should not be made on the basis of rumor and innuendo.
For these reasons, I think the PED issue can't be an issue in voting for admission to the Hall, even for those who got caught. The use was pervasive, and if it wasn't openly encouraged by MLB (they loved the MaGwire - Sosa HR race because it brought baseball back from the 94 strike), they certainly turned a blind eye and tacitly approved it. They are in large part responsible for the pervasiveness of PEDs. They cannot act holier than thou at this juncture. As for tainting the players from that period, unfortunately they all carry a taint. Molitor and others went in without any taint, but that is not fair. No one should be beyond suspicion from that era including Jeter. When all the crap was going down with MaGwire and Bonds and Sosa, there was a time when the press was heralding ARod as the player who would rescue baseball from the steroid era by re-writing the record books and doing it the "right way". They could not have been more wrong. Everyone should carry the taint from that era, and if their achievements are borderline Hall-worthy, it should count against them.