If you are doing a classic 2d platformer (which you [the OP] are not [this answer is directed at people who are doing it]) then you could use something like DragonBones (open source). Even in your situation, you could make some considerations and implement something like this.
If you must have the tool look perfect from a lot of angles and can't compromise on the variety of angles and authenticity then you need to make the animation in 3d, attach the tool to the animated model and render away (this of course would result in the texture atlas you wanted to avoid).
To get one image of a 2d tool looking good, you have to keep it bound to one plain. This means it cannot be moved very freely and will only look good when it's viewed from the side while most 2d rpg let your see the character from 4 - directions, this looks best when you can see the character only from the left or the right side of it.
You can also make one tool of each type, i.e sword, staff, mace and etc. , then use different color color palettes to get multiple similar but slightly different results.