I cannot say that we will get Kanto for certain, but I think there is a very strong likelihood that we will get it, because it is integral to the plot for GSC. First of all, the Pokémon league is located in Kanto, as you have to travel east of New Bark Town to get there. There are events such as the S.S. Aqua, Team Rocket sabotaging the Power Plant, Cinnabar's volcano erupting, Janine replacing Koga as a Gym Leader, Blue replacing Giovanni as a gym leader. There is also Professor Oak talking about a White Rock in Kanto during the Shaymin event in DPPt, which was not present in FireRed / LeafGreen, so I would assume they would elaborate on that more. Finally, there is Red going to Mt. Silver to train.
I think that if Nintendo were to remove Kanto from the re-make of Gold and Silver, they would be doing a huge retcon (changing the story of GSC dramatically). In order to make a maximum profit off of the series, they would have to not only find ways to please the newer generations of players, but also please the people that originally owned GSC. To me, being able to travel back and forth between both regions and gather up to 16 gym badges, and learn about what happened after Pokémon RBY was my most favorite feature of GSC.
I think HeartGold / SoulSilver is just as much of a sequel to FireRed / LeafGreen as Pokémon GSC was a sequel to Pokémon RBY. While other games simply had references to other regions, GSC was the only one that included one of the other regions entirely, and was a very direct sequel to the events that happened in Kanto. What would Pokémon Diamond and Pearl be like if it included Hoenn? While Johto and Kanto are connected by land, it would be possible to just have a boat connecting Sinnoh to Hoenn. If they did make Pokémon Diamond and Pearl that way, then Hoenn would have to be somewhat abbreviated, just like Kanto is in Pokémon Gold and Silver. Still, I think it would interest fans if that happened.
So in the end, I believe Nintendo will remake the regions to be faithful to Pokémon GSC, and to keep fans that owned Pokémon GSC, and liked being able to visit both regions, happy.