I have the following situation:
I have 1 Rails App that has 2 domains, each of these domains has multiple/dynamical subdomains.
This app is in AWS using a load-balanced Elastic
I think that the best solution for your problem is to have multiple domains on the same SSL certificate and then assign that certificate to your ELB environment.
(you can have wildcards, maybe that wasn't available at the time the question was asked)