Problem #1 is the shop letting that wheel go out the door in that condition. Use the right length of spokes or grind 'em down, but get those spokes flush with, or a thread or two shorter than, the nipple.
Problem #2 is the person taking the wheel back not recognizing instantly that the wheel was "incorrect" as if there is some sort of debate. The wheel is not usable in that condition unless you like getting flats more or less constantly. This is not a close call.
Problem #3 is not getting a call back when promised. The call should have been timely and should been a discussion about how to remedy the problem, for which I see two viable options: fix it or refund your money. Full stop.
I don't like to bash an LBS, but unless you get a call Monday morning and the result is them fixing the problem by the end of Monday, you should not let them wrench on your bike(s) ever again. They may be okay to buy stuff from, but if they don't back up their work, they can't be trusted to work on your bike.
At least that's how I see it.
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"I'm in shape -- round is a shape." Andy Rooney