Both ROTF and DOTM presents us Transformers do clone. As seen with the Arcee sisters and the Hatchlings on the Nemesis. One way I see bringing Megatron and stay dead is that Megatron modify a Hatchling to grow as a clone of him. Megatron 1 transferring his personality and knowledge perhaps a piece of his spark to the would be Megatron 2. It would mean Megatron 1 has a back up plan in case he is killed. Megatron 2 would emerge from the Nemesis and come to Earth. Heck he may even bring the Nemesis.