The difference is basically that the Soviets were killing millions of Orthodox Christians, but the Patriarch essentially agreed to look the other way, and make statements that made it sound like everything was perfectly fine. It would be like America today rounding up all the Jews and putting them in concentration camps that were designed to kill them while at the same time getting forced labor out of them, and murdering them in large numbers, and then the Jewish leaders of America, even though they knew what was going on, issuing statements talking about how they supported the American government. Basically, Sergius felt like he had two options:
1) Make a stand on principle, and be murdered like all the other ecclesiastics who didn't flee into exil or hide in the "catacombs".
2) Pretend like everything is ok, continue to live, and work for changing things and somehow holding Orthodoxy together.
So he chose option 2, and tried to hold the Church together by using some questionable tactics. I mean, obviously reality is much more complicated that I am saying here, but that's the long and short of why some consider Sergianism a heresy.