Warthog doesn't float in practice; the original 'Bronco' does, but not with all the modifications we made to produce the Warthog derivative. So as-is, they'd be sod-all use to the RM for what Viking is supposed to be used for. They're also a bit of a nightmare to operate, especially with the limited amount of integrated support they have compared to Viking (because they're a UOR). They do have their advantages over Viking (you're probably less likely to die in one for starters), but I given the choice I think the RM would probably prefer to stick with Viking. All the Vikings in Afghanistan were from the existing RM fleet, and were being used out there even if Marines weren't deployed on Op. Herrick.
Buying new vehicles and getting the Army's heavy cavalry regiments to operate them was the most efficient way to meet the long-term requirement for highly-mobile armoured vehicles: It stopped the RM getting pissed off by the CDS/MoD (or whoever is in charge of the overall UK strategy in Afghanistan), giving their only armoured vehicles away to other units, and leaving them with a reduced fleet for their own amphib requirements (particularly since a lot of their precious Vikings were getting blown-up or going BER by other means). The RAC also has a lot of people trained to drive heavy, tracked metal (a lot more than 3 Cdo. has trained Viking crews) but there are no CR2s on operations, so they were a more flexible commodity when given free-reign over the vehicles without having to drawn on elements of a smaller RM unit every troop rotation.
The RM's Vikings will apparently be upgraded with Mk.2s for free, because of the vehicles/parts we're giving to Sweden to meet their UOR for BVS-10s.