If you still like Owen, then it would be okay to atleast use it in the MN. Heck, since its a family name I think it would be okay to still use it as a FN.
In my DH's family, Joseph is a popular family name. One of his cousins is named Joseph after their gpa. My nephew's MN is Joseph (my DH's B's and SIL's son). Our next boy will most likely have the FN Joseph. We were considering using Joseph for this LO's MN but decided to keep it for a future FN and also wanted to use a name from my side first. It's a family name, no one owns it.