Jaina would alienate herself from the rest of the Alliance if she committed mass-genocide on the entire Horde. Or, at least, she'd alienate herself from the figureheads of the Alliance. People like the Council of three Hammers, Velen, Varian - and the biggest one of all - Anduin Wrynn.
Jaina is the biggest female role model for Anduin since his mother died when he was a baby, her influence on him has made him develop into the young man he is today. If anything is holding her back from remodelling Orgrimmar to look like what Theramore does, it's how Anduin would react to it. He'd never forgive her for ruthlessly murdering countless Orcs who, for the best part, are just honouring their blood oath to their Warchief.
Most of the Orcs involved know what they are doing is wrong, but they're oath-bound to do it anyway- Just look at Nazgrim. It's arguable that all of the playable Orcs are filthy traitors to their warchief- which is why it's upsetting that all of us are forced to partake in this stupid Darkspear rebellion.
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