The difference between the two is subtle but important, given that they both cost the same amount of points.
The Commissar gives the unit LD 9, stubborn, and an automatic pass should they fail, at the cost of a 3 point conscript. This is essentially fearless aside from being able to go to ground, at the occasional cost of a conscript. This is very useful for a shooting conscript squad since almost everything is AP5 or below. Even a 6+ cover save is Emprah-send. Even better for cover-campers.
The Priest gives War Hymns and Zealot. Zealot gives Fearless, so no going to ground or executing your own guys, and Hatred. War Hymns gives a 50% chance of doing something awesome in close combat. Fantastic for fighting in close-combat because your volume of dice just got even more amazing on the first turn of combat. Plus due to 50 conscripts and fearless you will likely last longer than a round of combat, so more chances to get War Hymns.
So if you find yourself using conscripts as a shooting unit, go Commissar. If they are used to charge and take charges, go Priest.
This is not definitive, just my thoughts on them without an experience.
Any other suggestions?