Threads per compute shader group
There shouldn't be any performance penalty inherent in using a 3D group over a 2D one, the dimensions are just an aid for programmers to map invocations on to memory locations (since you can read or write wherever you like). 

The group size affects which invocations can access the same block of groupshared memory, so it forces all warps from the same group to run on the same SMP. If you have a shader that needs to move stuff around a lot in its local memory block (e.g. a bitonic sorter), a large group size is preferable, but in your case it shouldn't make much difference. 

I suspect your problem is with the idle threads within your warps. If I understand your question properly, you're using a thread per input texel or sample to do the texture reads, but then only a subset of these threads to do the processing? If so, you're sacrificing a lot of compute power within each warp. Remember, texture reads are done in minimum 2x2 blocks, and the results get cached in a way optimized for locality for the dimension of the texture (see this question). So although your general purpose shader might seem slow with all the texture reads, a lot of them will be effectively almost free. Also, the GPU does latency-hiding on slow memory reads, swapping in other warps until the result of the read is available. So your general purpose shader actually seems like the smart option here, as it maximizes compute power.