Thanks a lot for the report! I usually don't run Factorio with sound turned on, so I didn't notice the sound-spam. :-)
I suggest to put in at least a fake swing animation that takes some frames to complete. It could also fix the loud sound issue.
For version 1.1.9, I copied the walk, walk_mask, and walk_shadow animations and added a value for animation_speed to the animations I use for mining_with_tool. However, I'm not quite sure whether the value I've chosen is OK. Would you mind trying this with different values? All that's necessary is changing line 16 of file animations.lua:
-- Modifier of the animation playing speed, the default is 1, which means one
-- animation frame per tick (60 fps).
local mining_animation_speed = 10/60
If you think that another value for mining_animation_speed is better, just holler and I'll update it for the next version. :-)