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For full context, see here: https://www.docdroid.net/hK45eJm/img-20170916-0001-new.pdf
The sentence in question is taken from line 14:
[内ヶ嶋]{うちがしま}[為氏]{ためうじ}とその[一族]{いちぞく}で、[白川郷]{しらかわごう}に[帰雲城]{かえりくもじょう}という[城]{しろ}を[造]{つく}った。
=> "It was Tameuji Uchigashima and this lineage who built the castle called Kaerikumo."
I interpreted the で after その一族 as the continuative form of copula です and aligned its tempus with the 造った.
Let me include the previous sentence:
しかし、15世紀後半に、ここにやってきて、住み着いた者がいる。
内ヶ嶋為氏とその一族で、白川郷に帰雲城という城を造った。
It seems like the subjects (主語) are left out in the sentence in question:
（それは/彼らは）内ヶ嶋為氏とその一族で、（彼らは）白川郷に帰雲城という城を造った。
「それ/彼ら」 refers to 「15世紀後半に、ここにやってきて、住み着いた者」("people who came here and settled down in the late 15th century") in the previous sentence.
So it'd be literally like:
It was / They were Tameuji Uchigashima and his family, and they built a castle called Kaerikumo-jo in Shirakawago.
You're right that the で after その一族 is the continuative form of a copula. So, grammatically speaking, you could split the sentence into two, like this:
それは、内ヶ嶋為氏とその一族だ（った）。（そして）彼らは、白川郷に帰雲城という城を造った。
...but I don't think a relative clause is involved here.
