Dave:
If you are staying in Livermore then Orwood would be your best bet as a place to launch. Here is the web site for the place:
http://www.orwoodresort.com As for hitting a rock: You would have a hard time hitting a rock unless you drove your boat into the levee. There are plenty of other things to hit, however.
The bottom is all soft mud, so just hitting the bottom is generally not too traumatic. A bigger concern is hitting a log or similar object floating just at the surface.
The tide causes all sort of issues. A spot that was deep enough to pass over this morning may become too shallow a few hours later. Pull your boat up on the beach to take a break and in 20 minutes it could float off or become so stuck that you will be waiting there until the tide comes back in. A log that was safely stuck into the shore can float free on a rising tide and drift back into harms way.
The only real hazard of the Delta is that the water is so muddy that you can't see into it to tell if it is deep or not. Any lake or river will have hazards, and they will not all be marked.
As for finding smooth water: no problem! If you ar there mid week you will find smooth water all over the place, unless the wind is just really howling. On the weekends you may get enough boat traffic on the major traffic channels that you will have to seek less traveled sloughs to find good water.
If you want to see some sights and you are going to be there a week then I would recommend trailering the boat to a few different marinas to put in. My favorite area of all is an area that is known as "the Meadows", which is on Snodgrass Slough norht of Stockton. The best place to launch is Wimpy's off Thorton road. Take I-5 north, past Stockton, exit on Thorton Rd. A few miles west is Wimpys. Warning: There is a LONG stretch of water way that has a 5MPH speed limit on it between any place you can launch and the Meadows!
If you happen to be there on the 4th of July there is a pretty good fireworks show put on right in the middle of the delta, right on the main channel at a place called Mandiville. For that you might be better off to launch at Hermen & Helens, as it will be a lot easier to find your way back in the dark!
I am sure you will have fun, so enjoy!
Rod