This may sound odd but the injury may actually help your pup and her SA. It sounds like she is going to have a long recovery time which will probably involve lots of giving meds, bandage changes, and trips to the vet. All of this means that you will be giving her a lot of special, undivided attention which will help you bond with her in ways that you would not have bonded without the injury.

Also, she is going to need to be on pain meds which should help keep her calm to facilitate healing due to the fact that it is a leg injury. The meds should also help take the edge off while she is crated. Discuss her SA with your vet so that they know she has the SA issue as it might interfere with her healing if she gets so upset that she starts digging or doing things with her leg that may make the injury worse.

However, injury or no, this is what I would recommend for the SA:

Put a crate in your living area where your family spends most of their time. Keep her crated and only take her out of her crate to potty or play. Of course, you want to make sure she is getting exercise and attention but she needs to learn that being out in the house is a privilege.

Feed her meals ONLY in her crate. Also make sure that she has plenty of toys/rawhides/etc in her crate. I cannot tell you what a difference feeding her in her crate will make.

You have to ignore her when she throws fits. Completely ignore her. She will not hurt anything howling or whining. Yes, it is annoying but any time you give her attention while she does it, she wins. She has to learn that noise does not equal attention. Luckily, the injury will give you an excuse to be firm and not give in to her tantrums.

She will learn that it is ok to be crated but it will take time. I cannot emphasize how important it is to be 100% consistent.

For more info, please read thisarticles on housebreaking and crate training. Good luck!