Thome played during the juicer era, so for one his stats really didn't stand out among all the big-heads (he only won 1 HR title, 1 RBI title and 1 OPS title) and secondly,
you can't really know 100% that he didn't juice too.
It's unfortunate that he is caught up in that a little bit, but it is what it is. Hopefully in 10-15 years things will be clearer and we will be better able to separate the real hitters from the druggies.