We looked at both options - booking through a
travel agent and also directly with Disney.
We actually met a wedding co-ordinator the year before while on vacation to have a look round the pavillion and discuss options (intimate/custom weddings, flowers, etc). Once back in the UK we then looked at our travel agents options.
We decided to book directly with Disney for a number of reasons.
Primarily we saw dealing with Disney more "direct" - we could email or call our co-ordinator any time and would get an answer back the same or next day.
After talking to our travel agents it appeared that they would pretty much act as a middle man - we told them something and they then contacted the Disney co-ordinator. We couldn't see the real benefit the travel agent offered us over dealing directly with Disney, so we decided to deal direct with Disney.
We thought it might be more expensive directly with Disney but it wasn't (Disney was a bit more expensive but offered a bit more as standard so it balanced out in the end).
Also, we changed a few things a few times! That wasn't a problem with Disney and there was no "changing" cost involved - there was with the travel agent we looked at.
The Disney co-ordinator also called us once a week to discuss options until we were happy with the general plan of things. Bear in mind this was an intimate wedding, not an expensive custom one. But with Disney it wasn't an issue - we never felt pressured into being sold options we didn't want - we decided what we wanted and Disney simply helped us choose.
Finally, i called our Disney co-ordinator an hour before the wedding to arrange a little surprise for my wife - it was done without an issue. Not sure how that would work if booked through a travel agent.
I'm not saying booking through a travel agent is the wrong way to do it (i haven't had a wedding through them after all, and i'm sure many people have booked through a travel agent and found it great), but i can say that we were VERY happy with the service we had talking direct with Disney!!
Why not contact both Disney and your travel agents and give them a list of questions and see how they respond and them make your mind up?