There is no indication that the VS relationship is going to end on October 24th when CO leaves SkyTeam. Considering the relationship that VS has with other *A carriers (SQ and BD) I just don't see that being a serious risk.

Be careful with the fare buckets; CO has limited earnings on some fare classes as of last December. I know that some Y classes were affected; I don't know about the J buckets.

And, obviously, the CO routing is the most certain to earn miles but it means the SFO-EWR flight potentially in a domestic F seat which isn't ideal.