I'm in a civil partnership too and I researched it inside out before conceiving, including consulting a lawyer specialising in lgbt parenting and legally both mothers (or fathers) have equal rights. In exactly the same way as a father has equal rights to his child. It's not like step parents at all, it's legally the same as a man and woman creating a baby (for couples married or in a cp). The law was amended in 2009 to include this.
That's in general terms, obviously Sophie in your case since she's being abusive she is forfeiting some of these rights so you'll be protected in that way, same as if a father was being abusive to the mother. She won't get custody if she's behaving like that towards you, just keep on documenting all her behaviour, I hope it works out soon for you.
I'm not contradicting your lawyer, who is talking about your particular case and the relationship you already have with Amelia, I just wanted to clear it up for posters who think that same sex non bio parents don't have equal rights.