It seems to me that you have to allow political parties to expel people if their beliefs are fundamentally at odds with party policy. It's obviously a difficult line to tread but if, for example, you styled yourself as the party of God, and you were promoting evangelical Christianity, and then one of your members turned out to be a Sikh who declaimed loudly that Christianity was nonsense, you'd be entitled to expel them, even though that person has a protected characteristic.
But obviously with the Greens, trans ideology is not a fundamental part of party policy, and people have the right to have different views on certain policies. After all, this is what parties do all the time - they debate a policy, then they agree a final policy position, and at the end there will always be people who don't agree with the new policy and will say so out loud. Lots of Tories, for example, are vocal about not agreeing with their party's policy on Brexit.