The headtube needs to be worked to as close as possible to the original round shape. If it was already reamed to size, reaming anew will remove more metal resulting in an oversize hole. It need not be absolutely perfect, since there's some spring to the metal, and will conform (within bounds) to the flange of the headset cup when it's pressed in.
If possible, reface the headtube to bring it to perfectly square, with out reaming (some ream/face tools make this possible using a non-cutting guide, others don't). That will ensure proper seating of the cups.
There's also another possible issue. It's possible that the same forces that flattened the tube, might have introduced some flex over it's length. If that's the case, the two pressed in cups will not share a common axis, which is critical to good headset function.
I suggest you consult another shop, but be very clear that you do not want them to ream the tube, because that will cause issues that will be difficult to resolve later.
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