Did they check the steering head nut torque? I checked mine at the first service, and although it was tight (about 40 ft-lbs), the spec is 85 ft-lbs.
Rebuilding forks at 12000 seems early unless you're running in really dusty environments.
Motion Pro is selling a little plastic/synthetic wiper tool that they say can clean up a seal and stop a leak. No first hand experience with the product, so I can't vouch for it.... but its cheap enough to be worth a try if you actually have leaking. My sense from your post is that you do not have an obvious leak.
Time and type of use can be more important than miles on fork oil seal life, but on 07 is pretty young.
I have seen older low mileage ST1100s that needed fork rebuilds.
You could check the fork oil. If there are parts that have worn to the point of needing a rebuild, I would think the fork oil would be showing some signs. In a one year old bike with 12000 miles one would expect the fork oil to look "ok" rather than the sludgy grungy look it gets after several years and a bunch of miles.
FWIW, its a messy job in my experience, and you usually need some special tools to get the fork fully disassembled (special socket on a long extension). Sometimes the Haynes manuals will give you tips on making special tools so you don't have to shell out the bucks for the official tool.
It could be a tire issue that they're avoiding because they sold you the tire and they would rather charge you for another job rather than fix the last job.
If the fork rebuild turns out to be necessary at 12000 miles, it would seem that it would be a warranty issue. I suppose technically bushings are "wear parts," But most folks would agree that bushings ought to last 12000 miles.