Thome only DH'd for 6 years out of 22~ seasons, and no, he was not feared more than Ortiz during his DH stint in the AL: 2006-2011. Let's compare stats from those years:
Ortiz - 3682 PA/3107ABs, .284 BA, .944 OPS, 143 OPS+, 78 IBB, 21.2 WAR
Thome - 2846 PA/2340ABs, .266 BA, .931 OPS, 142 OPS+, 43 IBB, 17 WAR
Not only was Ortiz way healthier with over a full season of at bats than Thome (767), but he sustained a higher batting average and OPS and higher intentional walk rate per AB (2.5% vs 1.8%), 4.2 more WAR, and 18 points in batting average. Thome's numbers are still very good for a DH but Ortiz added more value and sustained higher percentages over more at bats. He was the best DH of his era in the AL.
Regarding Ortiz' early years, not everyone gets off to a great start in their careers.
Is Ortiz the greatest hitter of his era? No. Non-roids, I agree that Pujols and other modern hitters like Miggy Cabrera are better and some other retired guys like Chipper Jones, Griffey Jr, Frank Thomas, etc. But the debate isn't about whether a DH should be the best hitter of his era, but that he is the best DH to fill that position among his DH peers. Ortiz was/is more feared in his era than current HOFers like Jim Rice and future HOFers like Thome. You may think that fear is unwarranted, but he beat Thome head to head over a 6 year span at DH. He's getting intentionally walked more than Pujols and Cabrera very late in his career. If he can keep it up until 500 HRs I don't have a problem with putting both he and Edgar in the HOF.
Regarding a DH in the HOF, the way I look at it is that it's similar to the closer. They only get paid for around 4-5ABs per game. Technically, closers are in the game even less than DHs, because not every game is close. The DH is in every single game. If the best closers are in the Hall, then so should the best DHs.