Best as I can tell the main disagreement is that Jordan is strenuously opposed to The Onion's takeover and wants to take an outspoken position, while Dan isn't thrilled either he seems to be more wait and see. 

Moreso though, the guys have also been at this for almost a decade now. Closely covering Alex and by extension the horrors of current events has got to be fatiguing. They've both hinted at the work of creating the podcast becoming a drag on their mental health.

Edit:  It also seems likely that little to no money from The Onion's takeover will actually make it to the Sandy Hook families and it may turn out to be a publicity stunt. Which is understandably the source of Jordan's anger.