Does the dad have SEN too OP? Crying when he leaves her isn't remotely normal, even for someone with anxiety and depression. I'm sorry for sounding predudiced and I don't mean it that way, but this kid is maybe going to have a huge change of having SEN too. So she won't "just" be raising a baby, but a baby with additional difficulties.
She'll be doing it as a single mother too, because let's face it, he's likely to bugger off when the going gets tough. He can't cope with saying goodbye to his girlfriend (who he's using as an emotional crutch, no doubt, a role she won't be available for with a newborn), who he also couldn't be bothered to ensure he didn't get pregnant. When men don't care about a pregnancy, it's because they don't see it, or the resulting baby, as their problem. There's no way he's going to be a responsible father, realistically. And I doubt their relationship will last once she's not pandering to him but to a newborn instead.
She's going to have to move out. If she doesn't she'll basically get no help from social services, they'll expect you to do it all. And she's realistically going to need a huge amount of support, essentially respite from parenting on a very regular and frequent basis, for this to have any chance of working at all. You already have a toddler. If she stays, you'd be taking on another baby, probably with SEN, plus the extra care and emotional turmoil of your DD, a teen who can't even look after herself without getting burnout.
There's no way she's looking after herself, her baby and a home, plus navigating the benefits system. It just isn't going to happen. There won't be enough support out there for her to make it work. So if you don't want to raise this baby as your own, it's going to end up in care due to neglect. If she goes ahead with the pregnancy, you're going to have to face the reality of the likely outcome and protect yourself emotionally, by detaching from her and the baby a bit. It's the only way you'll be able to remain your best self for your toddler, who doesn't deserve second best just because their sister got herself pregnant and made a foolish decision to keep the baby.
I think the best thing you could do right now is to tell her you don't support this pregnancy, she'll need to move out and go live in the councils homeless accommodation - because you'll give her notice to leave the house - and you'll give her what support you can, but you've got your own young child so you won't be able to help much at all. She'll hate you for "forcing" her (how she'll see it when she has to choose that to remain living at home) to have an abortion, but that's surely better than playing a part in bringing another life, a new baby, into a situation where nobody has capacity to adequately look after it.
The care system isn't a great place for a child to be. Even adoption at birth can affect people who are otherwise healthy and they can grow up with issues. If it's apparent the child has SEN early on, their chances of being adopted go right down. Nobody wants to take on trouble. Unless adopted at birth, this kid could easily end up in the care system for life. I wouldn't wish that on anyone.