Disable two-finger horizontal scroll
If you have disabled two finger swipes between pages in trackpad preferences then you should be able to configure it in BetterTouchTool by assigning keyboard shortcuts for those gestures. Swipes are generally fast and scrolls are generally slow. So you should be able to get both working side by side.

You can disable all scrolls if it really bothers you from accessibility section. In recent versions of OS X, disabling only horizontal scrolling is no more an option for built-in trackpad. Check this.