Just throw out the stats from 1994-2004 and judge on a per season basis who should be in based on what they did before and after. Bonds should still be in based on what he did for the first 10 years of his career. Clemens probably should too. You have to find a way to look past the cumulative stats merits and look at what those players were on average each year they were healthy. Or, you have to acknowledge that when everyone is cheating, nobody is really cheating and acknowledge those guys were still better than the other cheaters.
Yes, Bonds, Clemens, and Palmiero should without question be in the hall. Bonds and Raffy are probably the two biggest casualties of the steroids era, just based on what they accomplished. I think we can all agree that Bonds would've been a HOF'er without the roids. I doubt Raffy took them until later in his career, but at the time he joined the 3000/500 club, there were only four guys who'd ever walked the earth who had done that before.
Those guys should be in, definitely.
ETA: If I had to pick one that I'd leave out due to roids, it would be Clemens. Roids don't make you a better hitter or a better fielder, but they make you stronger and help you recover faster, which in my opinion benefits pitchers more than position players.