What was the compression of the other cylinders? If they are w/in the Good zone and no rod knock on start up you should be fine for awhile w/o a bottom end rebuild.

Is he positive it is a burnt valve or do the valves need to be shimmed? Shimming the valves should run you about $400 so you might consider that as a starting place. If the #3 exhaust valve is bad it wont cost you anymore start w/a valve shim because you have to remove all the intake/etc anyways.

You should be able to have a local machine shop check/rebuild the heads for the same price or less, call your local Toyota dealer(or closest one to you) and see who they use. The shop I used rebuilt my heads for about $500, which included new headbolts and a valve shim.

Make sure your mechanic knows he CAN NOT reuse the current headbolts, they are Torque-To-Yield(TT-Y) headbolts and are a one time use only headbolt. Reusing the TT-Y headbolts will guarantee a head gasket failure. You also have to use a new knock sensor and knock sensor wire, if you don't within a month of the rebuild your check engine light will come on and the code will be for a faulty Knock Sensor.

If you have the extra money I would also recommend sending out the injectors to be cleaned/rebuilt. There are some posts on here with links to injector rebuilders, if you don't have a local shop that can do it. Injector rebuild run anywhere from $7 for cleaning to $32 for a cleaned/rebuilt and balanced.