This might be SGM specific but you don't lose karma for killing your T buds with the C4, tripmines or the death station. The kills and the damage are logged but they're not "legit" kills, you don't see you killing 5 T buds in the end card when you have an unlucky C4.
The C4 is marked as "Avoidable" in the TTT gamemode code. Damage inflictors marked as Avoidable in TTT have a special rule regarding karma: if both the attacker and the victim are Traitors, and the death was inflicted by an avoidable inflictor, no karma is penalized from the attacker. So in short, no. C4 kills of Traitor teammates do not affect your karma. By the way: Tripmine and death stations are also marked as Avoidable.
Any damage/deaths between Traitors caused by a C4, tripmine or death stations have no affect on Karma. Anything else is working as usual.