ASHA, the professional organization for speech pathologists, looked into this question and prepared a paper on it. They released a paper and made a series of presentations revealing their thoughts. A summary of the research is found at: Oral Reading Fluency in School-Age Children Who Stutter. A powerpoint presentation of the research is available at Oral Reading Fluency Measures & Accommodations for Students who Stutter. A quick teacher-friendly version of the information is found at: Quick: talk Fast & Don't Stutter. Kathleen Scaler Scott's handout for teachers, Stuttering and Reading Fluency: information for Teachers is a simple explanation of recommendations as well.
The long and short of the answer is that for students who stutter, their oral reading fluency rate may need to be tested through an alternate manner. A speech pathologist should be consulted in determining how such modifications should be made and an IEP or 504 plan should contain verbiage clarifying the expectations of the student in regards to such assessments. This could mean anything from testing only silent reading fluency, having the fluency assessment completed by someone familiar with the oral speech of the student without being timed, to no modifications depending on student stuttering characteristics and the student himself. This is particularly important to consider carefully because stress tends to increase stuttering. A student who is aware that performance on the oral reading fluency determines reading group, progress advancement or grade advancement, is going to be under stress.
Of importance to consider is that stuttering is not the only language disorder that impacts oral reading fluency. Among these disorders are oral motor disorders and voice disorders. When testing oral reading fluency, teachers must consider all parts of the student that could negate the validity of the score. For those students, practitioners need to individually consider how valid the assessment results are based on multiple measures of performance.