This is tricky! I'm afraid I'm not sure exactly what you're asking with 1.
"I think him to be the murderer" is fine, though a bit ungainly. Here it needs to be preceded by "and". Your sentence 1a there is ungrammatical I'm afraid.
If he is the murderer, and I think him to be, we have done no more than is just.
I can't think of any way of omitting anything from that last phrase
2: all are grammatical. They all mean what they seem to mean? B and c refer just to one moral certitude, and a and d to more than one.
The difference between 2a and 2d is subtle. 2a suggests all these moral certitudes have collapsed all as one event, whereas 2d separates them, suggesting that they have collapsed at different times, or with different causes, or something like that.
I hope that helps?