In Eva, Humanity as a whole is essentially an Angel. Homura, being from a different universe, isn't. She also doesn't have an AT field, whereas Eva humans do. The way I decided to interpret things, Soul Gems have magical protection just like Eva souls have AT protection, but magic and AT fields don't work on each other. They're completely alien, literally from different universes, so when Homura entered Unit 01, the Soul Gem's magic field and the Eva's AT field just went "what the fuuu...?" and Homura's soul interfaced with Unit 01 directly. This caused it to go completely berserk, and because he was currently screaming and bleeding from several places due to being synced with two souls at once, Shinji couldn't deploy the knife, so Homura intervened and helped the Eva win so it didn't get them killed.