Yes I do believe that McGwire deserves to be in the hall of fame based on the statistics that he put up during his career.
I can understand not wanting McGwire in the HOF for being associated with steroids. However, if he is left out for that reason then you should also want to leave out any major league player that has steroid implications, including Alex Rodriguez, Roger Clemens, Barry Bonds, and Manny Ramirez.
My opinion is as the years go on there will be less of an emphasis on the "steroid era" and more on how a player performed compared to others in his career (i.e., McGwire's numbers should be compared to Griffey, Bonds or Thomas, not Mays, Mantle or Ruth). Eventually, McGwire, Bonds, and Clemens will get into the hall, though it likely will not be for another 5-10 years. Both the Mitchell Report and the Anonymous Survey in 2003 provide evidence that a high percentage of MLB players were on steroids.
As another poster mentioned in this thread, there is a lot of gray area between who used and who didn't before mandatory testing was put into place. The only guys who we know for sure used are the ones that have a) tested positive, or b) admitted to it. There is a level of speculation involved with anyone else that is accused of being on steroids, even McGwire.