Ruin the entirety of the triology? No.
Did it make it seem pointless? Perhaps.
Basicly... all the investment you did through the first two games, what Bioware kept empathizing as important, got thrown out of the window in the final game... -you don't do that!-.
However... I enjoyed the rest of the triology, heck until the last hour, ME3 seemed and felt like a true succesion to the series... I think that is why people got.. and still is getting this furious over how it turned 180 degrees out of nowhere.
Is it enough for me to damn the triology? Far from, but I can go back and redo ME1 and ME2... with lots of good times and excitement... ME3, I can't, even if I detach it completely and emotionally from anything i felt when viewing the ending: because I know that a replay of ME3 will leave no difference whatsoever. No consequences no alterations, just a one-trick pony.
So in short. Triology? Still good, very good.
Journey? Amazing.
Conclusion? Ambiguous, holed lore, and undoing of the triology's story.
So... I think that sums it up.
I can sit down with ME1, ME2... heck even Dragon Age 2 or some none rpg-title with 1 ending and replay it alright, because either it commits all the way in one-set-of-mind for where it is going, mechanical and theme-wise - wether high or low in content, predictable or not.
But ME3? I get a feeling of "What is the point of redoing that?"... it's a very strange feeling I haven't had for a game before... so I take that as a bad sign. The game gives you a taste of freedom... then strips it all away, everything but an fps aspect... and that leaves you sour.
But will wait and see what happens next. The journey was never anything but amazing.