Apologies if there are errors in the following, but this is my understanding...
Note that it was the Republican Congress and George W. Bush who converted this property to federal land. A ballot initiative to sell to the highest bidder had failed, and one to donate it to the federal government passed overwhelmingly (but was ruled unconstitutional). So Congress and GWB stepped in and took it at the request of the City of San Diego, “to save the cross” by making it federal.
Judge Larry Alan Burns earlier (2008) ruled in favor of the cross, but in January 2011, a three-judge panel of the Ninth Circuit of Appeals reversed his decision unanimously.
Judge Burns noted that the Ninth Circuit’s reversal wording pretty much tied his hands, making it clear that nothing but removal would be acceptable.* I believe that he felt that all he could do was issue this ruling that would pave the way for the SCOTUS to take up the case (that they’d previously declined). See his order here
I’m not so sure the SCOTUS will allow the cross to stand—even Justice Alito seemed against it from what I remember. Only time will tell, but my guess is that they’ll order it taken down.
*From http://www.utsandiego.com/news/2013/Dec/12/mount-solidad-cross-constitution-removal/2/?#article-copy:
Physically altering the cross was found not to be viable. In the end, Burns said he felt his hands were tied and there was little room to maneuver around the 9th Circuit’s ruling of unconstitutionality.
“Deliberate language in the opinion makes it clear that removal of the large, historic cross is the only remedy that the Ninth Circuit conceives will cure the constitutional violation,” Burns wrote in his ruling.
So in other words, the system is so entrenched in its anti-Christianity that no one can stop it or reverse it. We got precisely what the Founding Fathers wanted to avoid: a system fully unaccountable to the American people.