Can a school do so? Yes, should of school do so? Not necessarily. Colleges and Universities are supposed to follow a grievance process that complies with the Title IX Final Rule before the imposition of any disciplinary sanctions or other actions that are not supportive measures of the respondent. If a student-athlete is accused of a Title IX sexual harassment or sexual misconduct and they're suspended even on an interim basis from their sports team, separate from any NCAA considerations, schools often would suspend that student-athlete until the case is addressed and adjudicated.
The issue would be this is certainly, although not necessarily disciplinary sanction because the student-athlete has not been found responsible at this stage, it's certainly not a supportive measure of the respondent is definitely an adverse action that the school has taken. Whether the school is when it's within his rights to do so is a question that would need to be considered. It would be on a case by case basis and it would be case in fact-specific. If you're a student-athlete and you're accused of a Title IX issue or sexual misconduct allegation, the stakes are high. Having an experienced attorney-advisor in your corner from as early as possible in the process will help protect your rights and interests and they should be involved from as early as possible in the process.