Wouldn't you just delete your bookmarks on an iCloud device?
I mean, I don't know what's hard about this concept. ICloud is just and intermediary service. Once activated, it syncs devices. Obviously, the default option would be to merge, seeing as it doesn't really know which device is the one you 'prefer'.
Granted, they could add a few options during activation, say a box saying whether you want to merge, or just use what's on the cloud (I believe the calendar did that). I know it's probably too late now, but perhaps what you shuld've done is turn n iCloud n your device first, let it sync, then delete the bookmarks on the unwanted device, and then sync.
I understand merging is not necessarily the 'wanted' way that people want iCloud upon activation, but it's probably the single best default. Any other way leads possible data loss.
But I don't see why you want to edit in the cloud. Once on, editing anywhere is the same as editing everywhere. editing in e cloud is no different from editing n your device, UI aside.