I'm having trouble changing the bindings at all. Creating "Default (OSX).sublime-mousemap" in Packages/User isn't having any effect on the SublimeCodeIntel's default bindings.

This suggestion isn't about turning off reloads, it's about keeping the cursor position where it was before the reload. There might be another suggestion on this site for the problem you are experiencing.

This has been particularly painful for me lately as I've been switching a lot between a master branch and a feature branch the last couple of weeks. It's really annoying to lose where I am.

I'm totally fine with the line/char position being retained and figuring out the context switch from there. There's a much better change of being in the right area where as going to the top is almost never where I want to be.