Jua = anyway (finally)
Contoh: Kaya atau miskin, semua orang akan mati jua

Pun = also
Contoh: Saya suka ikan. Kakak saya pun suka ikan. 

Pun = just no meaning but we use to say something that shouldn't be like how it is
Contoh: Makanan tak sedap macam tu pun orang suka makan. 

P/s: Some things literally can't be translated or they're very difficult to translate. You will learn expression like this through watching a lot of Malay video or make friend with the Malay speaker

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Your question:
And so does it imply: (Therefore, just leave him be (anyway)./ Don't bother too much with him.(anyway)? 

My answer:
NO

Thanks so much Haniza!