In answer to the OP, no I do not think it was disrespectful of DT for reasons explained plenty of times in this thread already, most succinctly by bosk at the beginning.
But I'll tell you what I did find odd. The decision to play "The Shattered Fortress" as the second song on the Along for the Ride tour.
Why? Well, firstly, given that it was written as the conclusion of the "Twelve Step Suite" and very obviously a "big finale" type of song, to me it seemed a very strange setlisting choice to put it so close to the beginning without any of the other songs in the suite preceding it. But also, and perhaps more significantly, that song was really all about MP overcoming his personal struggles, and he had made it clear for years that the eventual plan was for them to perform these songs together live as one continuous piece. We all knew that. So, for the rest of the band to introduce that particular song to their live repertiore at the time they did, completely out of context, with no involvement of MP and thereby ruling out the possibility of performing it for the first time with him behind the kit (even as a one-off performance as a special guest), is a creative decision that I did not understand at the time and still don't, to be honest.
Yes, I completely understand and agree that just like ACoS, it is a Dream Theater song and I'm not by any means trying to suggest that performing it without MP was inappropriate. I certainly wouldn't go as far as to say it was disrespectful. They are free to perform these songs as and when they wish. I'm just saying I found it odd. It almost gave the impression that they wanted to make a point that as far as they were concerned, no song was "off-limits" anymore without MP in the band, a point further emphasised by the first live performance of Space-Dye Vest. And if that was indeed their reasoning, I wouldn't go as far as to say that they were wrong to do so. It just doesn't really make sense to me.