I'm sorry, but Couatl.exe can't "kill your entire FSX", it's just not possible, since it's an external .EXE, and external .EXE can't crash FSX, only a .DLL could.
What is happening, instead, is that your FSX has problems caused by something else (fact that you had to launch Couatl manually before was already an indication of this), which are the cause of both Couatl and other addons in the menu bar not showing, and Couatl is just another affected victim of it, not the cause.
Try to do a "Repair" for both FSX and the SP2