Going boom has little to do with deliberate rigging and more to do with Heisenberg's Uncertainty Principal. And if the transporter can grab people from miles underground and amidst the riot of lifeforms in the Amazon, then plucking someone from the empty lifeless void of space isn't going to be a problem.
The reason why they didn't solve the genocide is because the creators wanted it to happen on a meta level and didn't pay any heed to ways the problem could hqve been solved (fanwank it away as unless there are sattekites to bounce it off, the system is purely line of sight and the Watchtower was over the horizon). Or it may never have occured to the writers to use it as a solution (why worry about consistancy when you can Rule of Cool)