Out of context (and there are too many mentions of Cotta to find it in the index nominum), and without a citation, it’s difficult to see what’s going on, but it looks like this is part of an extended passage of indirect speech. The sentence itself is a question with a subjunctive verb (haberet), which is standard practice for questions in indirect speech. The verbs in relative clauses–here, dissentirent–and other subordinate clauses will be subjunctive if they’re part of what was spoken.
“What outcome did the plan of Cotta and those who disagreed have?”