The output seal is leaking? That probably a $20 part. I can't see that much in labor if they are talking about an output seal and a flush/fill. Get a quote from another shop or do it yourself. You can probably get the filter, fluid and seal for about $100. The most expensive part of the process is the tran fluid with Dextron at $5 a quart. You can rent an seal puller from most large auto parts chains and do the job in half a day. Unless you ran the fluid so low the transmission wouldn't shift, you shouldn't have any damage. You can add fluid to get it moved if you need to drive it somewhere.