If you've only got a few polygons that need work, use the Editor. There are a couple of ways to get this done. The fussier way to do this is to use the Reshape task (select the polygon that needs t conform and reshape it by tracing the polygon that is correct). I say fussy because that approach requires some finesse.
Another much easier way to do it is cut the polygon that needs to be conform such all but a small portion of that polygon can be deleted. Then use the trace tool to trace a new polygon that does conform, and then merge it with the remnant. You will also need to trace against the remnant polygon. When you do the merge, specify that you want to keep the attributes from the remnant polygon. It takes a couple minutes to deal with half a dozen simple to moderately complex polygons. That's a lot less time than figuring out the geoprocessing and subsequent QA (to ensure no unintended consequences resulted).
Thus, this would work well to reshape the Olympic Peninsula, making it conform to the geologic polygons.
You could also union
the two feature classes, and use the Editor to interactively merge polygons where the geology undershoots the shoreline, and select and delete where the geology overshoots the shoreline.