Stop them? No. Free speech isn't always pretty. Shame them? No. They have no shame. But it is possible to show them up, and to show support for the families of the fallen soldiers.
The gay-rights activists in Laramie, Wyoming had a good approach to Phelps and his zealots at Matthew Sheppard's funeral. Dressed in angel costumes, they showed up and silently interposed themselves between the protesters and the family. With their backs turned to the protesters.
I don't know if that level of theater is necessary, but forming a buffer zone to let the families mourn in relative peace would be a worthwhile counterprotest.
After giving this a little more thought, I've refined the idea a bit. Gather a group from the American Legion, VFW, maybe Boy Scouts. Have them walk in, single or double file depending on the number of volunteers, in step.
When they're positioned between the howling mob and the soldier's family, they stop. Right- (or left-) face, toward the family and turning their backs on the protesters. All with a minumum of noise and fuss -- If you've ever seen a military honor guard in action, they coordinate their movements with commands barely above a whisper. An amateur corps obviously won't have the level of skill of the pros, but it could take the same approach.
They then go to parade rest, remove their hats and lower their heads. And remain in that posture for the rest of the service. When the service is over, when Taps has been played and the family has departed, they return to attention and file out as silently as they came. If that doesn't show Phelps up, nothing will. Meet red-faced hatred with compassion and quiet dignity. Let the world see them in their wretchedness, and maybe some of them will begin to see it themselves.
ReignOfError
Stop them? No. Free speech isn't always pretty. Shame them? No.
That would depend on the location of the funeral. If the funeral is held at a funeral home located at the cemetery, the funeral home could bar them from the premises. Most cemeteries after all are private property. If they insist on acting up, they could be arrested for trespassing.