I was unexpectedly surprised by the interest that I had in these people who uncovered history with their bare hands, who saw what had not been seen for nearly two thousand years.

should it be, "...the interest I had in these people..."?

That is what I would say... However, I would also use"who with their bare hands had uncovered history that had not been seen for nearly two thousand years."

what would you say? would you use "that?"

Delete "unexpectedly" since it's redundant with "surprised." [Have you ever been surprised expectedly?]

The sentence is wordy. Here's my suggestion:

I was surprised by my interest in these people who uncovered history with their bare hands and who saw what had not been seen for nearly two thousand years.

Yes, it should be "the interest I had in these people" instead of "the interest that I had in these people." The word "that" is not necessary in this sentence because it is not adding any additional information to the sentence. When you remove "that," the sentence becomes more concise and flows better. However, this is a matter of style and can depend on the intended tone and context of your writing.