I would think the E-PL1 can ultimately provide better results due to the larger sensor but you must take into account some impressive features the S100 has like:
1080p video
larger and better LCD screen
much much smaller both with and without a housing.
f/2.0 lens ( not that much of an advantage underwater as you would most probably be shooting with strobes )
24mm lens (35mm equivalent)
Now , the other thing to consider is which housing for the S100 you are using. If you are using Ikelite that you dont have the back jog dial and then you are very limited when shooting manual. If that is the case , I would immediately say the E-PL1 is better, also because the Olympus housing is much more ergonomic and easy to use than the Ikelite ultra compact housing.
If you are using a Fix or Recsea housing for the S100 , then I would personally stick with the S100 and in a couple of years after you are ready to take it up to the next level go with a sony NEX-7 or similar.
If you use 2 good strobes and get the hang of shooting manual with the S100 , your shots will be superb and probably as good as most E-PL1 shots.
With that said , the E-PL1 optics are superior and with the S100 you can get some blurry edges and a bit of distortion especially when shooting 24mm at the widest zoom.
Good luck.
I'm going diving with the S100 this weekend with 2 Inon strobes , you can check our gallery after the weekend to see the shots from these dives.
gallery.housingcamera.com