I've always had issues with Bruce the time traveller for exactly the reasons you brought up. If BTT is bopping back and forth across the team stream, then he has to know that his Project is going to have a major screwup and be delayed 150+ years, which leads to etc.etc.etc. Its short of like trying to keep all of the Doctor Who storylines straight, sooner or later you have to stop becuase it hurts too much...
If you approach it from another angle, Bruce and the Council of Tommorrow, then there are several kinky twists you can toss into the pie...namely just who is on the COT. Simply adding someone like Albert Einstein into the mix can open all kinds of possibilities (just what was he working on for the last ten years of his life?). I can see someone gathering some of the US/UK political/military/industrial/scientitific leaders and convincing them of an upcoming atomic war. Simply starting this in 1952 or so will convience them
of the dire consquences of the Soviets getting the Bomb, the development of IRBMs/ICBMs. Many of these people would already be familiar with maintaining secrecy due to their involvement with the Manhatten Project, it would be a logical step towards the Morrow Project.
Submitted for your appoval...from the Twilight Zone!