By making more items available for gems in the mall, you are giving the F2P players a chance to slightly improve their odds against the gold users. Also, gems being removed from the economy will mean you have more gold users buying the gem packs and so on.
A simple example - the hero rebirth vials are critical for any player mid-game onward. By making it a gold only item, and worse, making it a non-tradeable item, you are generally restricting the F2P users to a max army of size 55.5k - this is ridiculously small when compared to the double rebirthed heroes who easily hold 250k+. The way battles work in this game, 55k of even the best defenders won't be able to stand against 250k of the worst offense. And I'm ignoring the fact that a double rebirthed hero will have MUCH better stats.
The pricing in gems could be similar to that done for quite a few other items - at a rate of 5x the price in gold or something. Not only will this help the non goldies have a better chance, it will also help stimulate the gem economy and act as a sink for the gems - this means more gems bought from the store. Also, you're getting more for the items than you normally would (the gem exchange rate in the store is at 3:1)
Sounds like a win-win, eh? Well, how about mall sales for gem items too? I'd buy up even more pioneer bags then!