I just implemented a solution for this that will be available in the next release.
The way it will work is this:
1. You will use 1 physical installation for all sites.
2. For any site where you want to use SSL, you will create a separate IIS site pointing to the same physical installation and use a host header to make that IIS site be used for the site you want to secure.
3. This extra IIS site will need its own ip address so you can bind the ssl certificate.
4. In user.config you will make a setting indicating ssl is available for that specific site like this:
<add key="Site1-SSLIsAvailable" value="true" />
where 1 would be changed to the site id of the site you are securing
Its this new setting option that will make this possible. Previously there was only one global setting SSLIsAvailable but with the addition of an option to configure it per site and by using additional IIS sites and ip addresses you will be able to secure sites on a case by case basis while still using one physical installation for all sites.
For others reading this, note that this solution only applies to hosting multiple sites based on host names. Multiple sites based on folders can already be secured with a single SSL certificate.
Hope it helps,