It feels like it goes all out at the last second to make the ending seem as open as possible. The MC is very clearly not suicidal, and she seemed pretty intent on stopping the other girl as well. My interpretation is that Sayaka might still be contemplating it, but Saki won't allow her to go through with it, and that they do intend to disappear and start over. Sayaka's "I don't know if this is the end for me or not" in the bonus chapter seems pretty clear to me. In the final few scenes we see that both Saki and Sayaka are carrying bags. I don't see why they would be doing that if they truly plan to kill themselves once they get off the train. Saki didn't have a backpack when she went to Sayaka's apartment (and it roughtly matches the one Saki has been seen with before), so clearly there was a trip made back to Saki's apartment before getting on the train, which wouldn't make sense unless she was picking up things that she would need to start over.
I think open endings are for cowards.
I think open endings are for cowards.