obama would never have the guts to authorize use of the systems in this way. His ROE will no-doubt let them get close enough to fire RPGs into the bridge.
Not really. First of all, you need to be able to direct the beam at the surface target that is close. This requires negative elevation angle. The radar may or may not support that; even if it does, the effective aperture of the array may be small, gain - low, beam - wide. This is because radars are, as you say, designed to detect space, air or far surface targets - not something within a half a mile from you. If the targets are that close you don't need a radar, you need a CIWS with performance of Metal Storm, for example.
Another problem is that the radar beam is not continuous; it is a series of very short pulses, with low duty cycle. So you might have a lot of energy in each pulse, but on average it's not that much. You transmit, and then you need to allow enough time for the reflected pulses to come back from the farthest distance that you support. This limits your duty cycle somewhat (there are workarounds.)
Yet another problem is that there is no "thousands of volts" of anything anywhere, and nobody would be electrocuted - not any more than your frozen chicken is electrocuted in your microwave oven. The only effect is that water (and bodies containing water) will be heated up. You can easily protect yourself by staying inside the ship; that is a generally good idea if you are speeding toward a warship :-) Even a thin aluminum body will protect you very well from any radiation.
Even if we take an attacker on an inflatable boat, and if that attacker doesn't wear any protection against EM wave, there is only a very limited zone where he may be in danger. That is close enough to the ship, but not as close as being completely in the shadow of the hull. But that's his destination anyway; he will speed through the dangerous area, and if he is still alive after that, he'll fix that by detonating explosives.
I think there is a very simple defense against swarming small boats: shoot at them until none are left.