This again has the possibility of just irritating the player, making them want to just reload to a far off save so they can get a better response. I'm going to admit, I do that all the time as a player (mass effect 1 and 2, Deus Ex are 3 particular games that come to mind). but it is an interesting concept. The problem is that players will enter your game with certain rightfully placed video-game-logic assumptions and video game tropes and if you utilize those specifically to trick them instead of clearly letting them know that all of their actions can and probably will have so and so consequences like in real life, rather than like how it is in video game land will will just drive them away.
So, basically, I'd say its important to let the player know before any consequences from their video game trope addled mind can be caused.
That is why I would only use it as a trope in the very first instance. I want to present the concept at the player in a way that they are used to seeing. I actually count on the fact of being able to re-load a save if they feel like re-playing up to that point is worth whatever change in response they wish to see. I don't see it as a punishment as much as it is a consequence of making that decision to go back and consciously re-play that portion of the game. By the same token, I would make the ability to save very open-ended so that the player has the most control over how far they need to go back. For short sighted decisions, this will work out in their favor, but I plan to also have decisions available with longer reaching consequences that don't show up until later. The effects won't ever be game breaking, but I would make certain it was absolutely clear how what was happening now is directly related to what decision the player made back then, rather than springing it on them as an unexpected punishment or simply a wrong type of choice. (heck, just to mock players that go back way too far with their saves to re-make a decision, I could easily implement a no-win type decision that requires a couple of hours of backtracking in order to realize that both decisions are bad)
Basically, I want to respect the player enough to not have to hold their hand through every decision they make throughout. Any type game is going to involve some sequence of decisions made in the heat of the moment, most of the time with only marginal expectation at what the actual outcome of that series of decisions entail. Video games often involve tools that operate outside the standard bounds of cause and effect, but they are all still played to fulfill a desire to go through and witness how your own decisions play out in hypothetical virtual settings.
As far as effectively punishing/rewarding players go in the context of the potential game I was discussing earlier, there are two things I want to prioritize above all else:
First, giving a game setting that seems entirely open ended initially, but actually has a short and relatively obvious path that steadily ramps in difficulty as it delivers the player to the option of entering the endgame, while not forcing them through a point of no return without clearly stating it as such. (this way, it would be possible to get all the way to the endgame with only the 3 free lives without even purchasing a single bonus life, then backtracking and getting a bunch of bonus lives all at the same time just for the endgame) Maybe even with options to advance through those stages even more quickly and having consequences for doing things that way instead. (Any areas outside of that path will be entirely optional, have clearly defined rewards, and ramp in difficulty based only on the player's current progress.) Or on the flip side, I can also provide a victory condition that can be achieved without playing the endgame levels, making them practically an optional affair just for players seeking that level of challenge from their game.
While the other being giving as much motivation as possible to play the game all over again with the possibility of exploring divergent paths where new decisions can lead to unseen options occurring. (which save-games could be used to exploit to an extent, but my game would be heavily class-based, so class based options would require starting the game entirely over as that class in order to actually observe and explore)