I re-watched the ending few scenes a few times and finally I notice what was out of place - it wasn't the the Statue of Liberty was Green or polished copper, it was THAT is was in the middle of the woods or park, not on an island. Which to me is a BIG FLAW: if as they suspect Walter Buried the pieces of the portal and then wrote down the GPS coordinates, then NONE would be there due to the Continental shifts of Pangaea. The GPS readings may not have been off by hundreds or thousands of miles, but SURELY they would not have been EXACTLY where he had them dig!
This leads me to believe that as Walter suggested, Peter indeed will go back to a million years to HIDE the parts of the machine and then change all history (if only slightly) and who knows "Peter" may exist but named David or Walt Jr. ergo Peter never existed. Something like that - the clips for upcoming episodes, especially upcoming seasons are very vague so they can diddle with the next seasons plot-lines.
I can't see a season without him, even if he were killed off, in Fringe anything can happen - except for Liv's FBI Boyfriend from season one, they had him ready to come back to life, then killed the character off - likely cause the story was going elsewhere quickly.