I would more likely understand Clark and Lois picking a name that has nothing to do with anyone they know, because most of us don't name our children after our folks (do we?). Lois and Clark would know full well that their child, being the first Kryptonian-human, would be unique and be treated as such with either a plain-jane name (which is, no offense, why Jonathan makes sense) or a unique name (nothing too unique as to be made up, or as offensive to one's ears as the babyname from the Twilight books / movie because I couldn't see Lois or Clark doing that to a child).
That's how I feel - that they would choose something unrelated to the family. That's why I went with original names when I've written the Kent children in (Michael, Hunter, and Rebecca). But, I could see them honoring the family with secret Kryptonian names, which would also keep that part of their heritage alive. So, Michael as Jon-El after Clark's Earth dad, Hunter as Jor-El for Clark's bio dad, and Rebecca as Marla-El (a mix of Martha and Lara). I see them more likely to honor Clark's folks that way since Lois' parents wouldn't even know about the secret Kryptonian names.
