Mike,
If you want to keep the members section independent of WP, how about a sub-directory instead of a folder?
members.mikesouth.com for example.
Since you are already using WP, why not keep the members area as part of it?
That's what I would do. There's a ton of great plugins for all kinds of members stuff.
If you go that route, I would use aMember (in conjunction with ccbill) for the payment processing.
We use aMember on
http://joannaangel.com with ccbill along with Joomla as the CMS.
Knowing what I know now though, I probably would have used WP for the CMS.