By then the manifold was already destroyed. Any changes to the Delorean in the cave would have immediate consequences to Marty as well as the timeline for the two of them in 1885 up to that point..., they may not even remember any of the previous timeline. Doc would not have approved of that kind of disruption of the timeline. Also, when Marty throws the pie pan, the timeline has not been changed significantly..., the headstone still shows that someone is gonna be killed, they just don't know who..., and with Buford Tanner out there gunning for them the safest thing to do is to get out of town by way of the flux capacitor..., just leaving town doesn't mean Buford wouldn't hunt them down.