They can just keep the new evolution-inducing items out of reach until you get the National Dex.
Ancientpower can safely be removed from Piloswine's/Yanma's level-up movepools, and Rollout from Lickitung's. Problem solved without any rude, unnatural FR/LG evolution halting. Honestly, that was one of the aspects I liked the least about FR/LG. It goes against the whole principle of new evolutions by new methods. (Law of Conservation of Game Mechanics.)
After getting your NatDex, areas in the Ilex Forest and the Ice Cave can open up containing the Eevee Rocks. There could also be Move Tutors in Kanto who teach the moves, Ancientpower and Rollout, limitless times.
Nosepass can be made to evolve in any crazy place they want, since you couldn't actually own one on G/S/C. Magneton would be a bit trickier. He'd need a special new room like I described for the Eevees.