Actually both prosecutors were Democrats...one with ambitions of becoming the US Attorney in Boston....would have been a nice feather in his cap to have the conviction of a US senator under his belt, not to mention significantly raising his level of esteem in Democratic circles.
Bottom line is you had Democratic prosecutors blatantly out to get rid of a senior Republican senator and acting unethically to do so. It was only during deliberations as a result of Stevens' convictions (in Feb 09) that the full extent of prosecutorial misconduct came to light. I give credit to AG Holder for having the courage to admit that the prosecution errored and effectively, absolving Stevens.
I suppose you could argue that the Bush administration should have recognized the misconduct before Stevens' conviction and taken action to replace the prosecution, but that's not very realistic. I can see the headlines on the Daily Kos now... "Bush fires Democrat prosecutors to hand election to Stevens"...