The right thing is to not remove the libglx.so file and just wait for a fixed update.
When I updated I ran into the same problem, however, I had about a dozen packages in the queue including mesa. So I just pinned the xorg updates, which allowed me to update everything else. Here's the error:
error: failed to commit transaction (conflicting files)
xorg-server: /usr/lib/xorg/modules/extensions/libglx.so exists in filesystem
Errors occurred, no packages were upgraded.
Whenever updates fail and you get an error message, it's a good idea to take note and report it, but it's generally never a good idea to manually intervene. Nine times out of ten the manual intervention won't work, you'll break something, and even if by some miracle it does install and work, it may prevent the future fixed update from succeeding.
At this point your best solution to fix your system is to look in your pacman package cache @
and look for the previous two xorg packages, xorg-server and xorg-common and reinstall them. You may have to force install them.
I hope this helps.