Phoenix is mad inconsistent, but I'd lean towards a Jean who is in control of the Phoenix Force being able to beat Wanda. Thing is, Dark Phoenix Jean wasn't quite that.
Probably the best source to go by is how Wanda and the Phoenix Five were compared in Avengers vs. X-Men. Wanda was able to beat both Magik and Namor when the Phoenix Force was divided between five mutants (they were terrified of her, initially). It wasn't until the Phoenix was split between Scott and Emma 50/50 that either of them had the edge over Wanda in that story (Wanda needed to team up with Hope channeling her power and the Iron Fist to beat Dark Phoenix Cyclops at the end of the event).
That said, Jean was trying to fight the Phoenix's influence over her throughout the Dark Phoenix Saga (Scott and Emma weren't throughout most of Avengers vs. X-Men). I'd think that one of those moments where Jean and Phoenix weren't on the same page would be all that Wanda would need to win.