So, how about those Separation-of-Powers issues?
Let's start from square one. Rep. Jefferson is being investigated for a reason, and he's not looking like an angel. I have no doubt that he'll pay, either legally or politically, for the actions that precipitated the search of his office.
However, the search was inappropriate under even the most basic separation-of-powers doctrine. What we're looking at is a member of one of the three allegedly coequal branches exercising authority over one of the other branches. Is it malicious? No, probably not. Still, it would have been more appropriate to delegate the search to the DC police force rather than involve the FBI in it, in order to avoid this exact appearance of impropriety.