The initial reports had the husband saying he had launched at Berkeley, and fished at Brooks Island..the water depth avgs only 5-7 ft deep [high tide] when heading to Brooks from Berkeley. This fetch of water is particularily nasty when the West winds are whipped up..the boat he had was capable of doing this, but extremly stupid if you ask me.
Secondly here is a blow up of the Marina. In this image the top of the picture is West-SouthWest.The launch ramp is locted at #6. This ramp remains open 24 hours a day. 
If I was launching at Berkley to dump a body, I wouldn't dump it in the "Marina". I would proceed North-NorthWest to near Brooks at night. I would then let the tide leave me high and dry. I would make sure that I would be refloated before daybreak by the next flood tide. While I was high and dry, I would take the weighted down corpse, and dig a hole in the soft bay mud. I would try and shuv it in as deep as possible. Lots of weight.
After a few tide cycles, this disturbance to an otherwise featurless flat would resume a normal look. Especially if it rained at low tide...
If the cops are looking actually within the confines of the Marina, I think they are nuts. With live aboards and what not...way to risky.
And Yes....there are several other areas nearby to launch: Richmond Inner Harbor, Emeryville, Alameda...