The answer is almost unequivocally yes. The school proceeding is a completely separate proceeding from any criminal proceeding. A school proceeding often moves much more quickly than a criminal case, so the school case often would take place much earlier in time than a criminal case would. The argument could be made, if the student is found responsible in a Title IX sexual misconduct case at the school and is later, say, found not guilty in a criminal case, that the decision of the school should be, say, overturned or reconsidered.
Arguably though, if a student is not found guilty in a criminal court does not mean that they did not in fact commit the crime or the offense. It's just that it means that they were found not guilty. That's a very complicated consideration. That's why an experienced attorney/advisor needs to be involved in the Title IX case from the start to help protect the student's rights and interests, to gauge the case, to advise a client as to what's going to be in their best interest. You have to take the necessary steps. Having someone in your corner from the start is critical.