In your situation, it's really six of one, half-dozen of the other. Usually I would say get the disc model, since upgrading to disc usually involves the added expense of changing hubs and/or wheelsets. HOWEVER, it looks like the v-brake-equipped Marlin has disc hubs already; so you would be free to upconvert for only the cost of a brakeset when/if the time came. The brakes that come on the disc model are the BB5s, which are fine brakes but really only about a $90 upgrade (or less even) any time if you shop online carefully.

So it's really just a matter of whether or not you want to justify having a very descent-but-not-spectacular set of mechanical discs right away.