Mac OS X Lion Server and Macports - Can they work together?
The short and easy answer is no - you can't just flip a switch to point all the Lion tools and scripts to the same (or similar) programs at a different path.

The longer answer, is yes - you can of course replace binary files, and test to make sure all the scripts work and patch any issues that arise either out of changed functionality or in the event that the Apple tools depend on a specific version of your web or database server.

Everyone I know that wants to install different software on top of Lion just turns off the Lion versions and controls the deployment with other tools like explicit paths, controlling the $PATH variable and alternate control and reporting structures.