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I'm sorry but with destruyeran it's almost agramatical.
You can write the paragraph from a present time of the story or from a past one:
"Y entonces pensaron «Si destruyéramos el corazón de la bruja, él perdería la inmortalidad»
"temían que si destruían el corazón de la bruja, él perdería la inmortalidad"
Just by choosing a past time of the story ("temían") you should leave imperfect subjunctive out. You're right about the conditional construction as a whole and the anecdotal bit telling they didn't do it, but anyway the fact remains all of that already happened and it's history -and you chose a past time frame to tell the story, that is, you are telling past events while you are standing in the present time-
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