Oh I completely agree with you. I think the Cubs should sign him and they probably will. I just find it highly unlikely that he gets traded. He is perfect for the Cubs and I agree with you in that they will most likely come to a deal. He just doesn't make sense to add to a contender at this point in the season based on his past.
Just for measure though, some players ERA's in their first three seasons with at least 20 starts:
Price: 4.42, 2.72, 3.49
Wilson: 3.35, 2.94, 3.83
Weaver: 3.91, 4.33, 3.75 (left his first year out which was 2.56 although he started 19 games)
Grienke: 3.87, 5.80, 3.47
Hernandez: 4.52, 3.92, 3.45
Bumgarner: 3.21, 3.37, 2.77
Wainwright: 3.70, 3.20, 2.63
Latos: 2.92, 3.47, 3.48
Cain: 4.15, 3.65, 3.76
Strasburg: 3.16, 3.00 (This is his third full year starting and has a 3.06 ERA)
The first group are all pitchers that pitched in the AL during that time in their careers, the second list all NL. Grienke is the only player who switched leagues. The AL pitchers averaged about 4.00 in their first three years and in the NL they averaged about 3.30-3.50. Grienke, with the exception of that one Cy young year has done much better in the NL then the AL. Samardzija would be looking like a pretty solid top of the rotation guy if he put up those numbers up in the AL. Not so impressive in the NL. Still, I agree he would be a good signing for the Cubs. They have plenty of money to overpay on a contract and he can pitch there for years. Plus they seem to really like him there.