To be honest, my first reaction is pull her out! But that's because I remember the misery when ds1 started preschool when ds2 was 6 weeks old. OMG, the endless colds (stuffy newborn is my personal hell), and the nervewracking nap/pick up drop off scenario. Having to wake a baby up from a nap to put them into the car to drive across town to pick up a child and then turn around and drive back was horrible. It sucked badly. And here all these people were talking about how putting ds1 in preschool would make my life so much easier with the new baby. Ha. It was the hardest thing I dealt with.
However, if she really truly loves it, I have a few suggestions, having been there and done that.
Obviously the best is to find someone to watch the babies or drive your daughter, but I'm assuming that's not going to happen.
About pick up and drop off - I did three various things: I would pull up out front, and call inside for one of the teachers to come out and get ds1. I would wait for another parent to be walking in, and ask them to walk ds1 in. When he was a bit older, I would park right in front of the entryway, and let him walk in on his own, while calling the teacher to confirm he was there and signed in. I did variations on this with pick up as well.
About germs - yes it's true that you can get them anywhere, but in my experience there is no greater breeding ground than preschool. I made ds1 wash his hands before he left the classroom every time I picked him up. I apparently was the only parent who did this, and they probably thought I was super paranoid, but whatever. I also kept hand sanitizer in the car and squired him when he got in (I know that stuff has it's issues, but I was desperate). As winter approached I bombarded him, the baby, myself AND dh with sodium ascorbate and another immune boosting powder my chiro gave me.
All that said, my personal opinion is that preschool is a lovely little playgroup, but not at all necessary. I adored the preschool that ds1 went to (also too expensive for us - MIL paid for it), but I regret sending him and chose not to send ds2. Obviously you know your dd and can probably gauge how traumatic it would be for her, but that's my two cents. Make the decision based on preschool as a fun activity, not as the foundation of her entire educational future. FWIW, my 3.5yo is more advanced "academically" than ds1 was at his age, and he's never been to preschool.
Good luck. I know exactly the difficulties of what you are going through. I shudder when I think back on that first year.
Edited to add: I just read your updated post. I would pull her, but I know I'm usually in the minority on this. She can still have playdates with her friends, but I'm not a fan of 3yos in preschool to begin with (having BTDT) and the hassle and stress just isn't worth it, IMO.
), but it just isn't the same to her. I would definitely NOT pull my child from a happy situation out of convenience, and I don't think the germ thing can be avoided.
