What cruise line was it? If it was a Royal Caribbean Cruise Line or NCL the price would have been the same no matter who he booked with. Unless it was a really bad agency who charges more than the cruise line price.
Carnival will soon have the same policy so it won't matter too much.
The only thing is what agency will give you extra "goodies" for booking with them. i.e. onboard credit, insurance or prepaid tips.
I believe in researching your cruise but I also know that some folks take it too far and become overwhelmed. If you get off on research then go for it but don't spend six months researching a seven day cruise. Unless you spend that six months on Cruisemates.