Yes you can. (This is basically BlaXpirit's approach but without the modification since it is unneeded)
Bindings that are done via a config file will not be shown in the game (the hotkey square is emtpy as if no hotkey was selected) but still apply.
To do this you need to go to your dota folder
dota 2 beta\dota\cfg\ and create a file called
autoexec.cfg. This file will be automatically loaded on startup from DotA2. (more on what autoexec is here: What is this autoexec.cfg, and what does it do?)
Next thing to do is opening config.cfg and copying everything containing
bind into the autoexec.cfg. After this you need to delete the old ingame bindings by going into the ingame settings menu, leftclicking on a binding and then rightclicking it leaving it empty.
The next time you start DotA2 the bindings from autoexec.cfg will be loaded automatically and this will result in blank ingame hotkeys. (I assume this is what you wanted)