Is it something that goes along with だからこそ and therefore means "because"? I know that this is one of the meanings of に but I'm not sure if this is the one used in this case since だから already expresses the idea of "because.."
Coming after 姿, the に functions as the same way as it does in ～にみえる and ～に近い. Basically 'in relation to ______' or colloquially 'as'.
だからこそ does indeed function as 'because' or 'especially because'.
瓜二つ is like saying 'Two peas in a pod'. I.e., having the same appearance or form as another.
そのおばは私の母に瓜二つだ - That lady is the spitting image of my mother.
そのおばは私の母にそっくりだ - [Same meaning as above]
Broken apart: お前の姿(Your appearance) に (as) 瓜二つ (strikingly similar) だからこそ (For that reason/that's why) むしろ (rather) 許せない (not forgive).
Rather literal translation: [He/She/It] has identical appearance to you. That's why I'd rather not forgive [you]!
Attempted figurative translation: I really can't let it go because he looks just like you!
If anyone else wants to tackle this one, the original text can be found here.