Unusual, yes, but not unprecedented. Mammoth at Holiday World (a similar "family" style waterpark raft ride) utilizes a lift where guests ride in the raft up the lift hill. Mammoth was built by the company ProSlide and Disney has worked EXTENSIVELY with ProSlide in the past (in fact, all the slides at Blizzard Beach are apparently built by ProSlide [
http://www.proslide.com/about-us/innovation-timeline/]. As such, it would make sense that this is a ProSlide attraction and thus guests riding in rafts up the lift would be proven already by the manufacturer.
Ground level loading also allows the ride to be ADA compliant (additionally, when you count the amount of time your on the lift in the length of the ride time, it makes a 30 second ride into a multi-minute ride which allows Disney to advertise the ride as being one of their longest ride duration water rides).