You can disable them by removing their entries from 'unlockables.xtbl'. Infinite sprint is called 'Sprint_zero_cost' and water running 'Sprinting_water'. You can also mess with 'sr3_city_objectives.xtbl' but it won't disable them if they're already unlocked, it'll only work with new game.so I haven't been following this mod in a while, but is there any chance of it disabling all of the forced upgrade unlocks from doing side quests (such as infinite sprint and water running)?
I'm not going to include this in the mod because it's supposed to improve the game and add new stuff, not completely rework it.