It's either that he died somewhere in the outside world, and has been reincarnated and then somehow got brought to Gensokyou... or that this is his kid.
These interpretations would be most dramtic and thus matching for the story. But it could also be simply a completly random child passing by, which looks like him. And thus she indulge herself in her nostalgic emotions. This would be narrativly a good way to portrait her still lingering emotions.
Anyway, it was a good move by eho, to let it be open for interpretation.
By the way: Am I the only one who diggs adult Marisa?