...Megatron will go back to the Cons in the near future? I remember hearing the rumor that the toy would include the faction chancing gimmick, but alas there is nothing. Is this a hint to the comics?
No. This toy was being designed long before the notion of Autobot Megatron even came into being. Before MTMTE even started. It was designed to be the ultimate Megatron figure. The figure comes with a sticker sheet that has an optional Autobot symbol on it anyway.
They're just stickers dude, but in a sense their's always going to be the stigma that once a Con always a Con.
The majority of the people that buy the toy don't read the comic. Marketing an Autobot Megatron doesn't make any sense. People know him as the Decepticon leader. Put his possible faction change in the bio story to explain the stickers or don't even explain it, just have them.