The day I was at San Jose (a Sunday in October), there were about 6-8 people on a very elaborate photo shoot. They were outdoors working in this area of the mission.....
I haven't been back since, so I don't know if the renovation is impacting the area where they were shooting.
One photographer and a couple were doing engagements along the wall/living quarters opposite the front door of the church. That area should be fine regardless of the renovation work. Play by the rules and you will be fine.