I read somewhere that the final episode(s) was already written down but Fox was sick of their shyt and cancelled it before it could be animated. Mary Jane ended up in 1776 during the American Revolutionary War along with Venom and Carnage.
That's not exactly what happened...the Spider-Clone thing WAS intended as the finale since the writers figured that would probably be the last season. But they left the Mary Jane thing open
just in case the show got renewed. But the writers have mentioned in interviews that if it had gotten renewed for another season, something like what you mentioned would've happened. With Spidey searching through time for MJ.
So basically it was just something the writers left open in case they unexpectedly got another season.