If the dealer really did split the cases without your permission, you don't need to pay them, and I would agree with the advice of dropping in unannounced and look for yourself. Best case, they're scamming you and never actually split the cases. If that's the deal, then simply take the bike and tell every local rider you meet about what happened.
If the cases are split, I would recommend you take all the parts and get out of there, but since you don't seem to have experience with the internals it would be easy to overlook some critical parts and as you know they're not cheap.
Doing this kind of work yourself is not like trying to build a nuclear reactor. A shop manual and a few special tools that are much cheaper than shop charges will go a long way to giving you the satisfaction of fixing it. You'll find plenty of help here, and come away with a better understanding of how the bike works. On top of that, you will do a better job than at least 90% of the mechanics out there because you care about the bike.
If it's split you'll really only need a crank install tool which you can get from RMMC, and probably the flywheel/clutch holding tool. If you screw up on assembly and forget something you'll need the case splitter though.
Check the review section for my comments on these. Also check out Rocky Mountain MC for 3 vids on case disassembly.
BTW, My kid had a shift roller fail on his YZ (known issue, well to all but me) and it sent small bearings and a collar through the tranny. He rode like this for quite a while until he blew the motor for a different reason. He later told me he wondered about the little bearings he found in the oil when you changed it.

His wonderment wasn't intense enough to ask me of course..
Point is even with that, the damage in the tranny was pretty minimal. I replaced the roller, all tranny bearings, and one cheap part I can't remember. the shift drum had a ding in it, but that didn't touch the fork tracks. If your gears were being damaged by bearing parts floating around, you would hear it. It's not a whirring noise. It's a gravel in the crankcase noise, even worser than a diesel!
I bet your tranny is salvageble.