By RAW, the undead will flee. The wizard will still have undead control once it stops running, but the Turn Undead effect will override that control, at least for a while.
Changing this would not be good. If a necromancer is attacking your group with an undead horde, then the cleric should be able to convert the undead without having to worry about an additional check to make the turn work. There are already mechanisms in place to make the wheels less prone to the undead (such as little deep or the dowry of the Bolster Resistance), so it is not necessary to add a new anti-twist defense layer. Also, the turn usually does not work against anything more than weaker enemies, since the more powerful undead have Turn Resistance and a lot of HD, which makes them difficult to turn.
In addition, the solution you propose (turn control vs. pitcher level control) is heavily weighted against the turn. A turn control is 1d20 + Cha, where a pitcher level control is 1d20 + pitcher level. Except at very low levels, the pitcher's level will almost always be much higher than the charisma bonus of a cleric, so this would make it very difficult to convert the undead controlled.