i think it's hard to know where to lay the blame, since all the bad elements were so intertwined; the sheer exhaustion from the multi-part storylines, the extra characters and subplots that went nowhere, throwing in the new warriors (wtf), creative team changes mid way, novice writers who couldn't handle a story of this magnitude, meddling from marketing, the constant stalling on establishing the new spider-man status quo (those scarlet spider fill in titles)...it was enough to drive jmd away, who was looking forward to being able to establish ben as the "true" spidey.
the revelation definitely had an impact but can we isolate how much of the ill will was directly due to the "truth" about ben? idk. long-term readers were split, new readers were possibly in favour. i feel like a lot of the push behind it was also the acquisition of future readers who wouldn't care.
i mean, we could also ask "would readers have been more receptive to the revelation that ben was the 'true' peter parker if it was handled competently"?
glenn greenberg's opinion was that it could have worked if executed correctly. his feeling was the opposite of what you suggest; that there should have been a bigger commitment to ben "taking back" the parker life, in that the character should have slotted in to peter's life seamlessly (no daily grind, no blonde hair etc) and it should have been done straight away.