Sentencing people to death in FS represents a purely militaristic feeling which is somewhat close to reality. I wonder, however, if at the time of FreeSpace 2 humanity would still rely on death penalties to solve problems.
Even now the validity/effectiveness of death penalties is questioned, and the number of countries that refuse it is increasing at an encouraging rate.
If we don't consider canon episodes like Bosch's anger towards the CO of the Sevrin, what do you think a civilized government and its military would be using when dealing with guilty people? Do you really think death penalties will be of any use in the future?
IMO, it depends on the situation. Although the mankind featured in FS2 is supposed to be much more advanced than us, death penalties could still be used in a number of situations, like (very) high treason. Overall, however, I doubt it'd be widely used because, IMO, it's always better to let people reveal as much as possible about the "issues" they were involved in. I don't see the point, for example, in sentencing a captive member of an opposing faction so early - interrogating him/her for a prolonged period of time may be of tactical importance.
Not to mention how captives can be exchanged with prisoners, other captives, and "favors". Imagine something like Bosch's request when he asks to jump unaided to Sirius.