There are two ways to stop a bomb from exploding, direct intervention and Security Scuzzers.
Simply hunt down the bomb, teleport it up into the pattern buffer and dispose of it. Placing it in a recycler with render it inert. So, oddly enough, will placing it in a Analyser. In single player you should pause the game before you go bomb hunting.
Combat EditBombs that are kept in the pattern buffer for long enough will explode as soon as they are teleported back onto the station. This can be used by teleporting the bomb near or next to enemies peeps, scuzzers or buildings. Since teleportation is only permitted inside your own territory this tactic is only useful against an enemy invasion or by teleporting the bomb right at the edge of your territory.