My understanding from the answers they gave at blizzcon was that if they can find a way to work the difference choices into HotS campaign they will but otherwise they'll go with canon, but it didn't sound like the choices would have much impact on the story even if they are worked in.
The choices seemed pretty irrelevant to me anyway, for instance the doctor one. If you side with her she's not infected, if you don't side with her she was infected all along. Seems kind of stupid.
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