It is a matter of different jurisdictions. The quo warranto petition is under the original jurisdiction of the Court. Approval or renewal of legislative franchise is the jurisdiction of both houses of Congress. As such, I see no conflict in jurisdictions.
As in the case of former Chief Justice Sereno, under Art VIII, Sec 5, Paragraph 1 of the 1987 Constitution, the Supreme Court exercises original jurisdiction over a petition for quo warranto, among other petitions filed by the State through the Office of the Solicitor General.
Hence, Solicitor General Jose Calida cannot be prevented from filing the petition in the case of the legislative franchise of ABS-CBN.
Likewise, Congress is not prevented from exercising its powers under the same Constitution to act on the application for renewal or a new franchise which is now pending before the House of Representatives.