And this is where your premise falls short. Destruction is not inherently chaotic and is not equal to Chaos. If you demolish a building to make room for another building and you use engineering to do a controlled implosion that doesn't make the destruction chaotic. Destruction != Chaos.
---------- Post added 2012-12-06 at 07:20 PM ----------
Why? The EC shows us that while Shepard is ascended he still retains some sense of who he was and his former self. The being that became reaper controller was ground in who Shepard was is still based on Shepard. You can't make blanket statements like Reapers wouldn't make the galaxy safe while at the same time accepting that the reapers are a tool. They are a tool to solve a problem. But like any tool it depends on who is wielding them.
Input | Output. In this case if shep is an assshole then expect the reapers to be assholes as well. If your shep is a good guy I don't see why the reapers couldn't be a force for constructive efforts.
As for the ending scene it's place is to do exactly what you saw at the end of the avengers although much more ambiguous. It's a teaser. Like the Thanos or the gang eating schwarma. It means to leave you with questions unresolved. All good works of art do this actually. In fact if you look through the history of narrative art you'll see that many of the greatest works of art are filled with holes and ambiguity and it's this that gives them mythological status.