Translation:I do not like this soup but I am eating it.
True. But "zupa" is feminine. And although you rather won't refer to soup as "ona", in other cases than Nominative there isn't really any other way than to use an appropriate form of "ona". So in this way it kinda works as a 'feminine it'.
According to your translation the second ja is I and nominative so I cannot see why you stick in a squiggle.
It's actually not Nominative. You need the second "I" in English, but in Polish repeating it would be redundant or even strange.
You can imagine "(Ja) nie lubię tej zupy, ale (ja) ją jem".
So as the sentence we put here doesn't have any "ja" (Nominative "I"), you only see "ją", which would literally translate to "her", but of course English won't ever refer to soup as "her". But Polish has to, because "zupa" is feminine.