Well, about Cloud reciprocating Aerith's attraction, that is up to the player, both the original game and the Remake always gives the player choices that either raise the affection points of Aerith, or don't, but also from a canon point of view, there are some hints that Cloud is quite into her, some examples:

1. Aerith starts with the highest affection points of all the "date candidates" (50 points) so most first time players will get her date as the default.

2. When they meet again after Cloud crashes thorough the church ceiling, Aerith offer to hire him as a bodyguard in exchange for "one date" and Cloud immediately accepts, this was the same Cloud that a couple of gameplay hours ago was telling the Avalanche guys that he didn't care about learning their names, since he accepted the mission only for the money, and would ditch them immediately after he got paid, the same Cloud that Tifa had to guilt trip with the memory of their "childhood promise" in order for him to accept a second paid mission. This same Cloud knew that the Turks were Shinra's top henchmen and professional assassins, and jet, he was willing to pick a fight with them just for a chance to spend some time with Aerith.

3. When Aerith got captured by Tseng, just after barely escaping alive from the destruction of Sector 7, Cloud does not say anything, he just immediately started walking, he had already decided he would go to rescue Aerith, even if at that point, he didn't even knew how, that is some pretty serious commitment to her.

4. In the Remake, he was literally left stunned and speechless by her beauty when he looked at her in the red dress.

Now about the answer of Cloud after the Gondola ride, I don't think he was rejecting her, is just that, in that point of the history he still does not remember that he had adapted some of Zack's identity and mannerisms as his own, so he literally is confused by Aerith's statement, and after that they don't have another chance to talk about their feelings, because Cait Sith steals the key to temple of the ancients and they are forced to immediately move forward with the mission to retrieve the "Black Materia" and that is literally the last dungeon they transverse together before Aerith goes alone to the city of the ancients and his murdered by Sephiroth.

Personally I don't think they need to change much to keep Aerith alive, Cloud just has to block Sephiroth's attack with his own sword, or just move Aerith out of the way, in the original scene he was close enough to grab her body before it felt to the ground, so from his position he had the chance to intervene.

The story does not need to change, because after all, Aerith is just a "rookie" Cetra, she was basically following the instructions of the "voices" of the Cetra spirits that were left at the Temple of the Ancients and in the City of the Ancients, but she herself does not know much about Holy, the White Materia or how exactly they work.

After avoiding Sephiroth 's attack, and destroying JENOVA LIFE, she could explain to her friends that she was trying to summon Holy, as instructed by her ancestors, but that she believes that she failed, because there was not any obvious effect or answer, (the White Materia in her hair could just fall into the water the moment Cloud move her quickly to save her, instead of the moment she is stabbed) so the party still needs to do the mission with Bugenhagen to review the scene in the waterfall "projector" and found out that Aerith was actually successful in summoning Holy, and that the reason there has no been any effect yet, is because Sephiroth is blocking Holy's movement with his gross alien tentacles. And voila Aerith alive no more changes to the story needed.

Final note, I agreed that Aerith was the one that commanded the lifestream to power up Holy in the last moments of the game in order to finally overcome Meteor, but she does not need to be death to do that, her prayers united with the prayers of all her friends and the wish to live of all the people in Gaia could have the same effect, and it will be completely within the "rules" of the stablished lore, the essence of "Final Fantasy" is that dreams come true, magic is real and the power of faith could make miracles happen... and that is precisely the beauty of it.