[Update, December 27, 2007:- The reporting storage of PerformancePoint 2007 server, i.e. operational and business reports location, is not supported on a report server that is configured to run in SharePoint integrated mode.]
I've been working with deploying and integrating reporting services into MOSS and wondered if it was possible to run my SQL2k5, sp2, reporting services in both native and integration mode, and posed this very question at a Microsoft Business Intelligence conference I attended a couple of weeks back. The answer was no, you can only run an instance of reporting services in either one or the other, i.e. native or integration mode. Naturally, when integrating reporting services with MOSS you need to set your reporting services to integrated mode. But what about if you have other applications where you want to still use native mode? A suggestion was made to create an additional 'instance' of SQL on the same server and then attempt to change that instance to the alternate mode. I haven't attempted this yet myself, but just thought I'd post as food for thought.