I'm assuming since you mentioned clerkships that you are going for DOJ or something along those lines. Your grades do have to be higher to get those kinds of jobs, but if you have something else going for you like Moot Court or law review it will even itself out.
From my understanding government positions are, generally speaking, not as concerned about your grades and school reputation when compared with private firms. The exception would be the high legal positions with the government like the US Attorney's office.
Please, any advice would be great. I have no idea what to do right now. I mean, I'm really good at actual law ... I received an A on my appellate brief, and in my internship I keep getting compliments on my briefs and research. But still, grades are everything in this career.