Your options for keeping your stash untouched are to whack them with your melee weapon (hold grip button to transform into the melee mode) or by shooting. There are a few items that give you more ammo, so your best bet is to just try to find treasures as much as you can. The battery pack that gives you 50 charge is a pretty common item that can be found around the island and even very close to the treasure chest.
Yea I think we should've maybe given the player a bit more freedom to use the weapon by lowering the firing cost. Now it's almost mandatory to save up on the ammo for those big waves of enemies. The original plan was to give the player some indication about where the battery packs are currently spawned so that getting more ammo wouldn't be purely based on luck, but unfortunately the deadline hit a bit too soon :)