You see, I can't give the words for a very simple reason. I am unable to find that exact Hadith in any book of hadith as this one is a copy and paste from another website and is not full hadith. Then very obviously this is translation as Muhammad (pbuh) did not speak English. However if I could find this hadith in Arabic then I might be able to understand a little bit more. Although Arabic is not my own language but it is a bit like my mother tongue Urdu. Because in Arabic words used make huge difference. Although that word might still be translated into one word only in English. I am not a scholar myself and my knowledge has limitations. I will try finding this hadith in Arabic and then perhaps I could tell you.
Just for example I will tell you that in English there is only one words "UNCLE" for someone that could be anyone. Whereas in Arabic there are different words for each of the person you may call uncle.
As for the main question (and I said that before) that ay hadith that contradicts with Quran then that hadith is rejected. And that is common rule.
Ok, here is the full Hadith,
Volume 9, Book 84, Number 57:
Narrated 'Ikrima:
Some Zanadiqa (atheists) were brought to 'Ali and he burnt them. The news of this event, reached Ibn 'Abbas who said, "If I had been in his place, I would not have burnt them, as Allah's Apostle forbade it, saying, 'Do not punish anybody with Allah's punishment (fire).' I would have killed them according to the statement of Allah's Apostle, 'Whoever changed his Islamic religion, then kill him.'"
Now on the face of it, this seems a very weak hadith to me for a very simple reason. Ali was Muhammad’s (pbuh) cousin and he was adopted in a very young age (around 10) by Muhammad (pbuh) and later on got married to Muhammad’s daughter. It seems impossible that he did not know about a capital punishment declared by Muhammad (pbuh) when he spent most of his life with him, and still he burnt someone. And then someone else is telling him that he shouldn’t have burnt those people but should have killed them.