too many variables to say which is cheaper (some agents have discounted deals due to volumes), but if you are getting round about the same price – I would ALWAYS book through an agent.
Reason being, if things go wrong, the agent will help sort it out. Think ASH Crisis airspace closures of last year – my company had various staff abroad, booked via our company agent and some who had booked directly with the airlines (we didnt have a mandate to use the company travel agent then).
Those who booked direct with airlines faced frustration of not getting through due to high volume of calls, those abroad had conflicting information and huge queses at airports – those booked via the agent (I was one) got a call from them asking what I wanted to do, and then they booked me overland (train) and a ferry back to UK, then a train to home once back in the UK. OK, it was a long journey home, but I was back days before those who booked direct with the airlines – and our company has now mandated the use of our company travel agent.