the thing about LBS is trust – you either trust them or you don’t. If you don’t you can either seek a second opinion from another LBS or do it yourself.
If you can’t do either option then you are stuck really.
I’d ask how much it would cost for him to rebuild a new wheel and then compare that with the cost of picking a new wheel up on sale somewhere.
If the cost is significantly lower then go with the LBS, if its close, I’d go with the new wheel, on the basis that someone who makes wheels for a living will probably make it truer than a local spanner in a bike shop (with the obvious exception of David Hinde).