I'm also considering an FZ1 as a eventual upgrade/replacement for my 2008 FZ6.
The FZ1 will without a doubt haul you around with less effort than the FZ6. The trade off for the extra power is decreased fuel range (smaller fuel tank, and less MPG's). Insurance costs are increased, tires are more expensive and will wear out sooner due to more weight and HP.
All that aside, I still think the FZ1 is a great bike. Just keep in mind that it has certain limitations. Regarding the FZ6 engine, I wouldn't worry about running it at 6,000-9,000 RPM'S all day long. That engine speed puts you right in the "meat" of the power band. The engine is designed to run up to 14,000 rpms, so you're not going to do any damage by running in the mid range.
Just run good fuel, and keep after your oil changes with high quality oil and the FZ6 engine will likely outlast your desire for the bike.