Refinishing pine floor

My wife and I recently had the pine living room floor in our new house
sanded to remove a number of indentations the previous owners had left in
it over the years. The sanding and the first coat of polyurethane was
done yesterday and when we got a chance to look at it after work, it
looked terrible. All the many imperfections in the pine are sharply
contrasted with the nicer areas. I don't know if the builder had just
used low grade pine, but there are a lot of dark areas that we don't want
being so noticeable, so we are thinking of going back to the dark stain
the previous owner had used. Any ideas as to (1) would the one layer of
polyurethane now on the floor have to be removed prior to a dark stain
being applied? (I am thinking yes), (2) what types of stains are available
that would be good for a pine floor and in this case would nicely cover all
the knot holes and other dark marks that the sanding couldn't remove, and
(3) should the professionals we hired have known that the pine floor was
going to look this bad before recommending a clear polyurethane finish?
We'd had to go to work during the day when the project was being done, so
didn't get a good look at the ready-to-be-sealed-or-stained floor, we only
saw it after the coat of sealer was already on it... Thanks for your
input.