Another and non tested approach may be changing the inbuild terrain shader a bit to support alpha, and then use the alpha channel of the lightmap to feed the alpha info to the shader. I made this quick mod of the inbuild FirstPassLightmap.shader file. I have not tested it for sorting issues and such, but maybe it could give some ideas to someone.
What you need to do to get it to work, is saving this shader in your project, and then quit and re-open Unity.
And then, obviously, make sure to use lightmap as your type of lighting of the terrain 
This is how the test looked:
Shader "Hidden/TerrainEngine/Splatmap/Lightmap-FirstPass" {
Properties {
_Control ("Control (RGBA)", 2D) = "red" {}
_LightMap ("LightMap (RGB)", 2D) = "white" {}
_Splat3 ("Layer 3 (A)", 2D) = "white" {}
_Splat2 ("Layer 2 (B)", 2D) = "white" {}
_Splat1 ("Layer 1 (G)", 2D) = "white" {}
_Splat0 ("Layer 0 (R)", 2D) = "white" {}
_BaseMap ("BaseMap (RGB)", 2D) = "white" {}
}
Category {
// Fragment program, 4 splats per pass
SubShader {
Tags { "SplatCount" = "4" }
Pass {
Tags { "LightMode" = "Always" }
Blend SrcAlpha OneMinusSrcAlpha
CGPROGRAM
#pragma vertex LightmapSplatVertex
#pragma fragment LightmapSplatFragment
#pragma fragmentoption ARB_fog_exp2
#pragma fragmentoption ARB_precision_hint_fastest
#define TEXTURECOUNT 4
#include "UnityCG.cginc"
uniform float4 _Splat0_ST,_Splat1_ST,_Splat2_ST,_Splat3_ST,_Splat4_ST;
uniform float4 _Splat5_ST,_Splat6_ST,_Splat7_ST,_Splat8_ST,_Splat9_ST;
struct v2f {
float4 pos : POSITION;
float fog : FOGC;
float4 uv[(TEXTURECOUNT+1)/2 + 1] : TEXCOORD0;
float4 color : COLOR;
};
uniform sampler2D _Control;
uniform sampler2D _Control1;
uniform sampler2D _Splat0,_Splat1,_Splat2,_Splat3;
uniform sampler2D _Splat4,_Splat5,_Splat6,_Splat7;
float4 CalculateVertexLights (float3 objSpaceNormal) {
float3 normal = mul (objSpaceNormal, (float3x3)glstate.matrix.transpose.modelview[0]);
// Do vertex light calculation
float4 lightColor = glstate.lightmodel.ambient;
for (int i = 0; i < 4; i++) {
float3 lightDir = glstate.light[i].position.xyz;
float lightAmt = saturate( dot (normal, lightDir) );
lightColor += glstate.light[i].diffuse * lightAmt;
}
return lightColor;
}
void CalculateSplatUV (float2 baseUV, inout v2f o) {
o.uv[0].xy = baseUV;
#if TEXTURECOUNT >= 1
o.uv[1].xy = TRANSFORM_TEX (baseUV, _Splat0);
#endif
#if TEXTURECOUNT >= 2
o.uv[1].zw = TRANSFORM_TEX (baseUV, _Splat1);
#endif
#if TEXTURECOUNT >= 3
o.uv[2].xy = TRANSFORM_TEX (baseUV, _Splat2);
#endif
#if TEXTURECOUNT >= 4
o.uv[2].zw = TRANSFORM_TEX (baseUV, _Splat3);
#endif
#if TEXTURECOUNT >= 5
o.uv[3].xy = TRANSFORM_TEX (baseUV, _Splat4);
#endif
#if TEXTURECOUNT >= 6
o.uv[3].zw = TRANSFORM_TEX (baseUV, _Splat5);
#endif
#if TEXTURECOUNT >= 7
o.uv[4].xy = TRANSFORM_TEX (baseUV, _Splat6);
#endif
#if TEXTURECOUNT >= 8
o.uv[4].zw = TRANSFORM_TEX (baseUV, _Splat7);
#endif
}
half4 CalculateSplat (v2f i) {
half4 color;
#if TEXTURECOUNT >= 1
half4 control = tex2D (_Control, i.uv[0].xy);
color = control.r * tex2D (_Splat0, i.uv[1].xy);
#endif
#if TEXTURECOUNT >= 2
color += control.g * tex2D (_Splat1, i.uv[1].zw);
#endif
#if TEXTURECOUNT >= 3
color += control.b * tex2D (_Splat2, i.uv[2].xy);
#endif
#if TEXTURECOUNT >= 4
color += control.a * tex2D (_Splat3, i.uv[2].zw);
#endif
#if TEXTURECOUNT >= 5
control = tex2D (_Control1, i.uv[0].xy);
color = control.r * tex2D (_Splat4, i.uv[3].xy);
#endif
#if TEXTURECOUNT >= 6
color += control.g * tex2D (_Splat5, i.uv[3].zw);
#endif
#if TEXTURECOUNT >= 7
color += control.b * tex2D (_Splat6, i.uv[4].xy);
#endif
#if TEXTURECOUNT >= 8
color += control.a * tex2D (_Splat7, i.uv[4].zw);
#endif
return color;
}
float4 VertexlitSplatFragment (v2f i) : COLOR {
half4 col = CalculateSplat (i) * i.color;
col *= float4 (2,2,2,0);
return col;
}
v2f VertexlitSplatVertex (appdata_base v) {
v2f o;
o.pos = mul(glstate.matrix.mvp, v.vertex);
o.fog = o.pos.z;
o.color = CalculateVertexLights (v.normal);
CalculateSplatUV (v.texcoord, o);
return o;
}
uniform sampler2D _LightMap;
float4 LightmapSplatFragment (v2f i) : COLOR {
half4 lightmapTex = tex2D (_LightMap, i.uv[0].xy);
half4 col = CalculateSplat (i) * lightmapTex;
col *= float4 (2,2,2,0);
col.a = lightmapTex.a;
return col;
}
v2f LightmapSplatVertex (appdata_base v) {
v2f o;
o.pos = mul(glstate.matrix.mvp, v.vertex);
o.fog = o.pos.z;
CalculateSplatUV (v.texcoord, o);
return o;
}
ENDCG
}
}
// ATI texture shader, 4 splats per pass
SubShader {
Tags { "SplatCount" = "4" }
Pass {
Tags { "LightMode" = "Always" }
Program "" {
SubProgram {
"!!ATIfs1.0
StartConstants;
CONSTANT c0 = {0};
EndConstants;
StartOutputPass;
SampleMap r0, t0.str; # splat0
SampleMap r1, t1.str; # splat1
SampleMap r2, t2.str; # splat2
SampleMap r3, t3.str; # splat3
SampleMap r4, t4.str; # control
SampleMap r5, t5.str; # lightmap
MUL r0.rgb, r0, r4.r;
MAD r0.rgb, r1, r4.g, r0;
MAD r0.rgb, r2, r4.b, r0;
MAD r0.rgb, r3, r4.a, r0;
MUL r0.rgb, r0.2x, r5;
MOV r0.a, c0;
EndPass;
"
}
}
SetTexture [_Splat0]
SetTexture [_Splat1]
SetTexture [_Splat2]
SetTexture [_Splat3]
SetTexture [_Control]
SetTexture [_LightMap]
}
}
}
// Fallback to base map
Fallback "Hidden/TerrainEngine/Splatmap/Lightmap-BaseMap"
}
If you want to use more than four textures for the terrain, you will have to mod the AddPassLightmap.shader file as well… 
