Following CopyCat's suggestion I used scnhacking.exe to remove the bomb from the mission. Changing entity 3344 removed the detonation and the abrupt ending of the game. Changing 3349 removed the associated warning message. In both cases the value of the "target" field was changed to "00".
From a command prompt:
scnhacking -e 3344 target 00 missiont.scn
In the missionobjectives.dat file the following line should be commented "//" to remove the "Locate and defuse explosive device" objective in the mission.
Officer DefuseBombs 1
Alternatively, the count can be changed from "1" to "0".
A better methodology might be to use the existing MissionT files to create a whole new mission. What software is used to compile mission files? Worldcraft?