Keeping the membership of two subdomains totally separate isn’t easy, though depending on the level of customization differences between the two sites, it may be possible for you, at least to the front end user. It does require a lot of creativity. For example, you’d need to hack the backend in order to assign new members to a different group based on which site the register from. And while you can create custom templates, in order to restrict their display to a particular group, you’ll likely need to run the membership templates through the standard templating engine. Even something as simple as ‘view members’ will need to be customized.
In short- it’s something you would probably spend a lot of time on and ultimately members are not completely separated. Search and Membership are the two tricky spots when it comes to running multiple domains on EE. I’d carefully weigh the time, effort and need for complete separation against the cost of two licenses.
