Is it better to be a Heathen to use the runes?

It's a partnership. No need to worship them, just be respectful when asking for their help. Then thank them afterwards (obviously).

I don't worship anything or anyone myself, but I do ask Inari to help me with some things in life, and she seems alright with me not leaving food behind on an alter or bowing to her image. So long as I respect her and her existence.