I guess the best way to think of it is like OOT vs SE--I mean does it really matter if Hayden Christensen is in ROTJ or not? The original is still the original. But its nonetheless bothersome that it was written over in the first place. And changing slightly significant parts of the EU, like the Jaster Mereel storyline, invalidates the ability to suspend your disbelief that it's a plausible, connected universe, since if you want to continue to pursue stories you have to mentally disconnect large chunks of it.

Such is the nature of a body of work that was made between two other bodys of work (the OT and PT) whose writer does not care acknowledge the existance of. As much as was possible the EU writers were forbidden to tread on prequel turf since Lucas knew he would be going there, but a lot of unforseen elements got developed in the prequels--case in point, Boba Fett was added because of his popularity in EU.