Hi John. Thanks for the great question.I know you're already aware of this, but I will state it again for anyone else reading this.
s2Member is NOT compatible with Multisite networking yet. This is definitely coming soon though.
I would expect to see this ready in
s2Member Pro v2.0+.
Now, that being said. Yes, your strategy sounds like a good plan to me. Keeping all of your own sites together in one install, and putting all of your customers into another installation should "hopefully" not cause any conflicts with the future version of s2Member Pro. Hard to say for sure at this point, but if I were doing it myself, that is how I would handle it as well.
It really depends on how you're planning to use it though. There are many issues that we're working through, which are causing conflicts between s2Member and Multisite mode. Many of the issues are security related.
One of the most troublesome, is the way Users are stored in the database table when Mutlisite mode is enabled. So just some food for thought... if you ARE going to need to have ALL users in one table for different reasons, I would NOT do two separate installations of WP 3.0, but rather, keep everyone in one Multisite installation. That way, once s2Member Pro comes along with Multisite support, you will have everyone already in the Users table, under one roof.