So, my original answer was incorrect. I am keeping parts of it here because it will be helpful for those with the same question; my answer will tell them how not to approach or think about the problem.
The most obvious and valid reason why Harry says "Well, I take it you're not sorry?" is this:
Griphook isn't sorry (i.e, he does not regret) that Harry saved him!
This was correctly pointed out to me by Badzen in the comments. This is something I originally did not agree with (specifically because I don't see why anyone would regret being saved). I was wrong, and I apologize.
Indeed, no one would regret being saved. And that is the point here—Harry is being sarcastic. I missed this.
Here, "sorry" means "feeling sorrow, regret, or penitence" (Merriam-Webster).
Instead of thanking Harry straight away for saving his life, Griphook beats around the bush by saying things like "You buried the elf", "You dug the grave", "You also rescued a goblin", "You brought me here. Saved me." Griphook keeps saying how he thinks Harry is unusual. This means that Griphook feels Harry is different than rest of the wizardkind, and he is thankful that Harry saved him. But Griphook isn't going to say it out loud.
Harry can't bear that digression anymore; he is impatient to ask Griphook for something. And that is why Harry sarcastically comes up with that dialogue to dismiss Griphook's antics.
Think of it this way:
"Well, I take it you're not sad that I saved your life, eh?".
Or this way:
"Well, I take it you're sorry [that I saved your life]?"
Note: After Badzen pointed this out, I actually went and asked this question in Science Fiction and Fantasy SE— What did Harry mean when he said ... —to see that others think. That "regret" interpretation is totally valid.
Here are two explanations from my original answer. Note that these are not the intended explanations of the actual context, but my efforts to make sense of "Well, I take it you're not sorry?"
"Rancorous" means "having or showing a feeling of hate and continuing anger about something in the past" (Cambridge).
Griphook does not like wizards. He absolutely hates wizards (note the generalization).
"Being a goblin, Griphook severely distrusted wizardkind and hated wizarding arrogance, stemming from the fact that goblins had been treated brutally by wizards in the past. Griphook had a somewhat barbaric and savage personality as he [a] enjoyed the idea of pain in lesser creatures, [b] was eager to harm wizards ..."
Source: Harry Potter Wiki
(1) Griphook isn't sorry that Dobby, a lesser creature, died!
"Griphook ... enjoyed the idea of pain in lesser creatures [like house-elves] ..." - HP Wiki
When someone dies, people who know them feel sorry. Here "sorry" means "feeling sadness, sympathy, or disappointment, especially because something unpleasant has happened or been done" (Cambridge).
Everyone is sad because Dobby died. But Griphook isn't. He always enjoyed "the idea of pain in lesser creatures" like house-elves.
Griphook is probably disgusted that Harry dug the grave with his own hands (as opposed to with magic which would be much easier) for a lesser being like a house-elf. Griphook did not approve of this act.
Harry said, "Well, I take it you're not sorry [that Dobby died or was killed]?"
You can say 'I take it' to check with someone that what you believe to be the case or what you understand them to mean is in fact the case, or is in fact what they mean (Collins).
While this explanation is a true fact, it isn't relevant to the context of the scene. This was pointed out in the SFF accepted answer.
(2) Griphook isn't sorry that he hates wizards!
"Griphook severely distrusted wizardkind and hated wizarding arrogance, stemming from the fact that goblins had been treated brutally by wizards in the past. Griphook ... was eager to harm wizards ..." - HP Wiki
One would expect Griphook to be sorry after Harry saved him. Here "sorry" is "used to say that you wish you had not done what you have done" (Cambridge). While Griphook did not literally harm the wizards physically, he wished he did. He wanted to harm them.
While talking to Harry, Griphook sounds "unexpectedly rancorous."
"Because of the prejudice Griphook had witnessed, he was amazed by the respect Harry Potter had shown to creatures such as elves and goblins. This was most apparent when Griphook observed that Harry buried Dobby ... Despite this, Griphook was unable to fully overcome his distrust and hatred for wizardkind" - HP Wiki
As Harry notices Griphook's rancorous manner of speaking, Harry asks
"Well, I take it you're not sorry [for thinking ill of us wizards, for being distrustful of us, for wishing to harm us, even after I saved your life]?"
"No, Harry Potter," said Griphook, ... "but you are a very odd wizard."
Griphook thinks Harry is a very different kind of wizard; he isn't like the rest of them. While Griphook is "positively affected by Harry's display of humility and love", he stands firm on his beliefs. He is not sorry for how he feels about wizards, and for his attitude towards them. He is not sorry for being eager to harm wizards (as can be seen later in the story by his betrayal).
