Chaplin may be acting like he's gone insane in order to ensure that, should the government manage to take back the Colorado, his crew will be exonerated (or at least receive a lighter punishment)—they can hardly be held responsible for his actions in this case.
The Colorado's "warning shot", in order to have been visible both from D.C. and New York City, must have detonated just off the coast of New Jersey. In the coming months tens of thousands of innocent American civilians would likely be dying from radiation effects, never mind the ecological impact and long term viability of the area.
About 200 miles off the coast, to be exact. As one of the characters notes, dozens of nukes were set off in the Nevada Proving Grounds, which are even closer to Las Vegas than the warning shot was to D.C., with no apparent side effects in Las Vegas. Weather patterns and ocean currents in the area would take the contaminated water away from the coast, and if the blast was an airburst there wouldn't be any fallout in any case.
The senior commanders of all of the armed forces (except the Air Force) are conspiring to launch a military coup to remove the President. Granted, the President was undergoing the impeachment process when the series began, and likely would have been removed by Congress even without the Colorado incident, but given the sheer blinding loyalty most of the military has shown thus far in the series, isn't this a setup for civil war? Would the series have explored the Colorado's involvement in the subsequent fighting between different factions of the Navy—those who supported the President and those who supported the coup?
Santa Marina is going to be seized by some world power and exploited. Most likely the Chinese, since they were already attempting to do so even before the Colorado was destroyed. That never turns out well for the natives and definitely wouldn't for James.
Then again, it is a NATO surveillance post. The Chinese would be entering very tricky diplomatic waters if they tried to take the island. They were only emboldened by the Colorado incident; with that resolved, and the US able to place its full attention on China, any further Chinese exploitation of the island will be much harder for them. On the other hand, there's good material for a follow-up series where James leads the islanders in a resistance movement against whoever decides to move in.
