This is more of an event issue. If you look at the FAQ it has a pause function on it.
Ashley gives you a nice blurb from one of the tutorials on the site
Delta-time and framerate independence Delta-time and framerate independence You can set the time scale to 0. This stops all motion. It's an easy way to pause the game. Set it back to 1 and the game will resume.
You might notice you can still do things like shoot using the game controls. You can get around that by putting your main game events in a group, and activating/deactivating that group as you pause and unpause.
Basically whatever events you have running that can still be clicked on and destroyed need to be in a group, or just place everything in a group and deactivate it on pause.