You still have access to a lot of tools by playing non-lethal — there's a pretty wide variety of non-lethal weapons and items in every category. And you can also use lethal weapons for other things (e.g. distracting people, destroying things in the environment, kneecapping/stunning guards before CQCing them, shooting off helmets...). You can use a lot more than 5% of your arsenal.
Also, the game definitely rewards you for not killing people and being stealthy as the rank bonuses can be pretty massive - you also get rewarded with better staff. But it's designed in such a way that you can also achieve the highest ranks without being stealthy and by playing lethally - you just have to be extra quick and/or compensate by doing extra mission objectives.
Ha, and you also get to avoid being constantly covered in blood if you play non-lethally.
Overall it's a well balanced game and it doesn't punish you for playing one way or the other (within reasons I guess).