Having recently been to Cabo (last October) I can tell you that you will be off the ship long before noon on a tender. I was on Radiance OTS and we arrived in Cabo at 9am. We had tix for the boat tour out to Lands End late in the afternoon and we were off the ship about an hour and half after the ship dropped anchor. Granted... you wont be first off the ship, but you will be off before noon. Excursions usually are off the ship within an hour. Usually, if you have paid for a excursion with private operator, the cruise line will let you get off in time to make your tour.
Cannot tell you about which beaches may or may not be crowded, but you might check into the beach resorts and hotels in the area. They might be your best option at finding a nice quieter beach with the amenities for which you are looking.
I don't recommend taking the ships excursions out to Lands End as they are way overpriced. Most are about $40. When the ship departs Cabo, you will go right by the Arches and will get a great opportunity to take great pictures from your balcony or the deck. As far as sea life around the arches... don't plan on seeing any while on the tours. There is so much activity in the area, any sealife has forced out by tour operators.