While 1 Gal down on
Hyd is not good, i don't think you damaged anything and those noises you are hearing is just you being overly cautious. The
Hyd system worked, as you used the tractor. So that means nothing was left exposed (dry pump). If you had drained too much the
Hyd system would only partially or completely not work and, well, that would be ugly.
Only thing I can think of is a bit of a heat issue (oil does not cool as well as there is less) but that would be a big stretch.