Ok i'm fairly sure the the RAW on this makes it a flat no but not really being an expert on these things I thought I would throw it out here to the crowd.
Channel Smite (Combat)
Source PRPG Core Rulebook pg. 119
You can channel your divine energy through a melee weapon you wield.Prerequisites: Channel energy class feature.
Benefit: Before you make a melee attack roll, you can choose to spend one use of your channel energy ability as a swift action. If you channel positive energy and you hit an undead creature, that creature takes an amount of additional damage equal to the damage dealt by your channel positive energy ability. If you channel negative energy and you hit a living creature, that creature takes an amount of additional damage equal to the damage dealt by your channel negative energy ability. Your target can make a Will save, as normal, to halve this additional damage. If your attack misses, the channel energy ability is still expended with no effect.
Channel Element (Su): At 4th level, a Jistkan magistrate gains Elemental Channel as a bonus feat, choosing the elemental subtype that matches his blessing. He doesn’t gain the ability to harm undead with channeled energy (if he channels positive energy) or heal undead (if he channels negative energy). Instead, he can channel a blast of elemental matter and energy that buffets his targets. The Jistkan artificer’s blessing determines the damage type of this attack, as indicated by the table below. A successful Reflex save halves the damage.
Now as the magistrate cannot channel positive energy to harm undead or heal them can he channel smite with fire instead?