Additional suggestion, it might be better to limit leaning to when the player is stationary or walking. Currently you can jog and lean. Though, with staminacost it would be still possible to retain the current gameplay on those servers where aim and movement are main focuses, as these servers have unlimited stamina

Agreed!

I agree, these two things feel unnatural and do not fit in the game. Many players bind lean to the same buttons as Move Left and Move Right, which makes them automatically lean when they are moving side to side. In my opinion the best way fix the lean issue is to slow down the movement whenever the player is leaning. This would counter the keybind abuse as it would slow you down. This is the way it used to be in ArmA 2 too.

For the prone spam, maybe stamina consumption and accuracy nerf would counter it.