Ja soboie tak po przekładam
I think she goes there- I thought she went there
I think she went there- I thought she had gone there.
Widziałem też różne przykłady z "realized" gdzie dużo osób miło że jeżeli kontekst jest jasny to nie użyją perfrct np.
I think you're looking at this the wrong way. Don't ask if a tense is right/wrong. Ask if it says what you want it to say. Think is not necessarily an ongoing process. In my first bullet example above, it's a single thought at a past moment of time. And the past perfect is often not necessary. For example: "I didn't notice at the time, but on reflection I later realized that he [had] kicked her." Had will make the order of events totally clear, but without it the order is still clear from the context.