Unite is definitely the way to get your cut path. Now I assume each one of those, hmm, I guess we'll just call them "leaves," is an individual object with it's own fill? If so, I would clone everything twice, that way you've got three copies of the artwork inside a single document.
I'd turn the bottom one off and lock it so that I have something to go back to once I've shot myself in the foot.
I'd use the Unite operation on the middle layer to make my cut path.
On the top copy I'd select everything and then use Object->Path->Offset Path, set to something fairly low like 0.125", then Inverse Select, and then hit Delete. Theoretically, this shouldn't have too much effect on the gradients inside the leaves since the size adjustment was very small, and any crazy transparency effects should remain intact since all you've done is just pushed the paths out a little bit.
Again, this is theory. Not actually having access to the artwork I don't know precisely what you're dealing with, but under the right circumstances it should work. At the very least I hope it sets you on the right path.
