Let’s get the usual “separation-of-church-and-state” argument out of the way first. Securing the Pope, whoever he may be, is a State responsibility and no one in his right mind should be arguing against it. No one should begrudge the Catholic faithful among the citizenry the opportunity to at least see the Pope in person either. If providing that opportunity requires declaring January 15, 16 and 19 holidays, then by all means should those dates be holidays.
The point is that neither assuring the Pope’s safety nor providing Filipinos the chance to see him impinges on the Constitutional prohibition against “respecting an establishment of religion.” What does are those State actions that would mandate, say, prayer in public schools, or making one’s religion a condition for State employment.