Well yeah. And the whole screaming girl thing basically suggests that Moriarty had a lookalike/mask, and Watson being hit by a bike made him all dazed so he saw what he was expecting rather than what was actually there.

Alternatively, the plant matter earlier in the ep is from a plant that can be synthesized into a paralytic (from the original stories). Holmes lands in the truck of bedding where Molly is waiting, bloodies up, takes the paralytic, and rolls onto the street.

But he'd need some way to prove it was him. Either the paralytic, and real Sherlock in the morgue, or a body from the morgue goes into Sherlock's coffin.