(yay... I register just to answer this question... le sigh....)
Well... if you think about it, you are given the option of offing both Morgans. Plus, you don't have to play Furture Past 1 or 2 to get the good ending in 3 (as far as I am concern.) Plus, if nothing else, the Morgans, in the end if you let them live, will get "punished" by Grima at the end. Assuming that the Outrealm warriors are responsible for giving the Future Past timeline a chance to survive, I'm pretty sure dead is the punishment for the Morgans. Not to mention... they were in hoods and shady, therefore the other children would have not known it was Morgan leading the Risens.
As for the two Morgans being in the same timeline, they can just off that Robin had twins.... and both are called Morgans... and only one was able to make it through the time portal.