Molly-jane has a middle name and a last name... so same thing.
I dont think it sounds funny, unless you plan on calling him buy his full name frequently...
Also people will shorten names... its frustrating, but something you have to deal with.... Molly-Jane which i often type as MJ, but NEVER call her that, is called MJ, Molly and most annoyingly Mol.
Name you child what ever you want.
I have a friend that had 4 middle names as her mum couldnt choose!