As far as i know your character account isnt permanently linked to steam at all. To use a non steam version of heavensward though you will have to buy a non steam version of "a realm reborn" and link both of them to your SE account on the mogstation. As far as i know this should work.
Dont know if this is possible but you may have to unlink the steam version from your SE account. If this is nescesary tech support should be able to help you.

I'd love it if anyone could confirm this.