Ideally, you don't want your main app server being tied during file uploads (both to the app server and subsequently to S3).
CORS (Cross Origin Resource Sharing) exists to avoid precisely this. You can upload the file to S3 directly from the client-side and let amazon worry about handling multiple uploads from your concurrent users. It lets your app do what it does best without having to worry about the uploads themselves.
This SO question discusses the same issue and there are several customisable plugins like fine uploader out there which can wrap around this with progress bars, etc.
This completely removes the need to make use of any kind of queue. If you need to do certain bookkeeping operations after the upload, you could simply make an ajax call to your server after the upload is complete with the file info, etc. It should also address any concerns you might have with instances being removed due to autoscaling since everything is client side.