Removing plot points seems like a story quality issue to me, but I digress.
I haven't read the script leaks, and I don't plan to, so is this "Prothean" character really that important, or are they another Zaeed/Kasumi? Are they really a Prothean ? In ME2 it was mentioned that the Collectors were highly altered and no longer resembled their ancestors, like in the beacon visions in ME1, so it might not really be what it's claimed to be.
Though if the script specifically states that in fact, it is, then surely it's better for such canon-altering DLC to be just that, optional DLC?
afaik they're just another zaeed/kasumi