The Vice President can't tell the secret service how to protect the President. Only the POTUS could instruct the SS to alter the route, and it would still be extremely hard for them to do that.
Actually, LBJ and the Texas democrats he led did much of the planning for the trip. The Kennedy administration, other than LBJ and his cohorts, knew very little of how things were done in Texas and which groups Kennedy should meet with, where he should go, etc.
This is precisely why, if LBJ had a part in sending the motorcade through Dealey Plaza, none of this is either surprising or incriminating. All of that is notwithstanding the fact that Dealey Plaza is a large pedestrian area (for a parade where Kennedy was wanting to be seen by normal folks on the street) on a major thoroughfare out of downtown. Would anyone bat an eye at someone routing a motorcade parade down Poydras to I-10 on its way out of downtown New Orleans? No, because it's a logical and commonly used departure route.