GSX works just fine with FSX:SE, and it surely hasn't "screwed up" your sim.
That might have happened is, instead:
- You ALREADY had either your DLL.XML or EXE.XML corrupted by other add-ons faulty installers, or by having edited it by hand
- The GSX installer tried to fix it, but it might have been beyond repair, like in a illegal format (yes, we know of installers doing that)
It would be useful if you could post your DLL/EXE XML files located here:
%APPDATA%\Microsoft\FSX
ZIP them together and Attach them to a post, and I can tell you what's wrong with them.