The protocol allows to not use 3G for data-traffic with the "backup-flag" (MP_PRIO-option in RFC 6824).
Or, it is also possible to simply not open up a subflow across 3G and only create it after the phone lost the WiFi connection. MPTCP supports break-before-make scenarios.
It is simply a question of instructing the kernel to do one or the other through some kind of configuration interface (may it be sockopts, sysctl,...)