Even with the "two separate signals" as you said it, Must Carry still, even in that case, only required carriage of one of them. MSOs are required to carry only one signal of a broadcaster. There is no requirement to carry sub-channels.
What I was saying was that pre-transition, analog and digital were two separate signals, so if the law only requires the carriage of one signal, then it made sense that only one, either analog or digital, might have been carried. However, with DTV, there is only one digital signal, main and sub-channels are just the way that the one signal is divided, and not separate signals.