Siphoning it down is going to be your cheapest simplest option, as long as you only have a two or three inch stream running out of the siphon you wont hurt anything down stream and probably wont even be able to notice it, during rainy weather I'm sure there is a lot more water then that flowing away behind your pond, with a two inch line it would be days siphoning down.
Unless I'm missing something, like maybe it would run right thru somebody else's back or front yard, that might complicate things a little.
That being said, theoretically if the liner is floating it means the pond is holding water just fine beneath it, if the pond beneath it was leaking you would think the liner would be sucked down tight to the bottom. Might be able to just remove it and see what happens. Good Luck !
