Look, if this were almost any band other than DT, it wouldn't be an issue. Didn't Metallica rip off Motorhead? Or every doom band ever rip off Sabbath? Or every power metal band rip off Iron Maiden? There's a reason that those bands are influential - people are inspired by them. Heck, DT has inspired lots of musicians themselves. And here's another thing, this is not the core of the DT sound. BMUBMD is not one of the better, or more representative songs from the album. He was inspired by the song, and then used it. More power to him.
Seriously, it's only because there is a cadre of hard core DT fans who are super into musicianship and take DT very seriously (and that's a good thing), that this is even an issue. I was actually trying to explain the Thiago controversy to my buddy (who owns a number of DT albums, BTW), and he literally looked at me like I was crazy. This is all blown way out of proportion.
Now, the real story here is the Portnoy thing. Seriously, people just need to ignore him. It's gotten to the point where it's just not worth it.