Hi Irini,
The mouse responses are only handled by eprime when the mouse device is added as Input Mask in the active E-Object (such as as slide). If it's not included, EPrime will ignore mouse clicks. The MouseDevice object can also be programmed using inline script, for example to show or hide the cursor. (The EBasic manual contains examples for doing so.)
However, you mention that you would like to prevent program crashes. In my experience, EPrime will crash as soon as it is not the active program on the desktop anymore. This can happen, for example, if you have two displays attached to the computer, and the windows desktop is extended across both. Any mouse click on the second screen will cause serious problems. The same happens when you accidentally press a key on the keyboard that causes another program to become active (like the Windows key). I'm not sure if there is an easy workaround for this because Windows handles such key and mouse presses itself, even if ERun is active. I know there are tools to disable certain key's system wide, but that won't be an option to disable the mouse at specific time points during the experiment. If the second display (if any) is indeed the problem, the easiest workaround is to disconnect or disable the second display before starting EPrime. Another option is to use the second display in EPrime to display a dummy Text or Slide object. (The multiple display option is available in EP 2 pro).
Best
Paul