Syrris:
The main downside that I can think of is that it could be an issue if if the 'gray' side jobs tend to involve a lot of shotgun/gunboat diplomacy, and not so much because of the lethality (although there is that) but due to medical/repair costs being prohibitive.
Seems like there should be ways to work around that. Since it's a game known for lethality, the potential issues of dead or incapacitated characters should be considered in advance anyway. If a character is killed or is damaged beyond usefulness, there should be a way to replace them quickly.
Also, it can be perfectly realistic for the goals of any opposing sides not depend on the utter destruction of the other side. That can still leaves "injury" as a potential issue, but it can put the focus more on just nullifying the opposition, rather than completely obliterating them.