Well, you've come to that timeless used car owner crossroads. The way I would look at an expensive repair is this: you're paying $2500 for a car that you know the history of. If you sold the car right now as-is, plus the $2500 and bought another car you'd be getting into a whole new mess of issues that you don't know about.
$1k for the transmission
$150 for the clutch
10-12 hours $90-110/hr in labor to R&R everything isn't
that outrageous... the numbers add up, more or less.
Are they replacing anything else in there too? Like the throw-out bearing, rear main seal, transmission shaft seal(s)?
Also, ROFL@ 'new from dealer transmission for $1500.' You can't possibly be serious about that, can you? MSRP on a new manual transaxle is
$3500, listing price at ~$3100.