Yes, good cards can negate good cards. However, Sites are always neutral, despite using the good brigades, but they can also be negated by good cards.
There are no special targeting rules for negate - if it fits the criteria in the ability (in Behemoth's case, "opponent's card"), it can be targeted by the negate.
Also, negating a Site doesn't remove the LS - the ability to hold a LS is part of the nature of the Site and isn't something that's negateable.
Finally, Sites are always accessible by any Hero of the same brigade as the Site, so every Hero would have access to Goshen if it was a Site. The Rainbow (full multi-color) Sites (Ends of the Earth, New Jerusalem, etc.) are primarily used to give access to other Sites (or for their abilities) rather than holding LS, as they don't limit who can rescue the LS.
