Really, how much harm could this possible do to the band? It's not like DT fans are going to hear about this then suddenly go "what the FUCK, Dream Theater? I may or may not have been ok with the countless other times you've done this sort of thing, but this time I'm through!" They're not going to lose their Grammy nomination over this. This isn't going to sully their name with the general public, since the general public still pretty much has no idea who they are outside of the fact that they recently got a Grammy nomination.
It's not going to do anything other than cause a stink that people will forget about after a few weeks and will only be brought up as another reason for people do dislike MP. It's a non problem; just MP fueling the flames again.
Anytime someone does damage to someones artistic credibility it's a serious thing. Sure they may not be fan-less over the ordeal(s), but at the rate MP keeps chipping away at DT they are going to be so badly wounded in the minds of fans/potential fans that they may avoid them altogether I don't think it's a dire situation or anything, but you can't deny the effect of public image on selling your goods. If it wasn't important the world would be an entirely different place.
DT is getting a lot of negative exposure lately, and for a band that didn't exactly have a massive following that is going to hurt them eventually. Now the accusations of plagiarism and copying their own songs are constantly going to be brought up as another reason to hate on them and it undermines all of their music as people are more likely to look for things now that they've "stolen" or "copied". MP's smear campaign, whether intentional or not, is working (look on the RED video atm at the people saying essentially "omg portnoy said DT ripped off this song"). Before, when people said stuff about DT copying songs or whatnot it was by posters and wasn't usually put up in a hugely negative and confrontational way or published as "news" articles (to my knowledge). They were stuffed in forums on the net and most people would have never heard about it. MP has starpower and a pretty large following listening to his every word while he stands on his soapbox of social media and forums though.
Also, it would sully their name with the public
because the public doesn't know who they are. All they will hear (theoretically) is the condensed little sound-byte that DT accused of plagiarism, and that's all they will remember. If they ever see something DT in the future they will probably look at it not as favorable (they had no sway at all before, and now they have negative thanks to the accusation, they certainly wouldn't like them more because of plagiarism!)
Anyway, it's not a huge deal either way, but it isn't something that should be downplayed. It has a real effect on their fan-base and careers as well as the public perception of their music.
I just wish people would stop exaggerating how similar the songs are for their own desires or bias - including MP.