If applications from the play store reading your SMS messages bothers you, then I can recommend using something like CyanogenMod's Privacy Guard (which exposes a feature called App Ops that seems to be a part of Android, yet hidden), or Xposed framework's XPrivacy (which gives you very fine-grained control over what information/permissions apps can and cannot access).

XPrivacy is difficult to configure without reading the documentation.

Both of these things require root.